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 55 -m 225 -t 32 -o /local/genbank/workspace/reads.spadescorr.k55 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.k55 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: [55] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /local/genbank/workspace/reads.spadescorr.k55/tmp Threads: 32 Memory limit (in Gb): 225 ======= SPAdes pipeline started. Log can be found here: /local/genbank/workspace/reads.spadescorr.k55/spades.log ===== Assembling started. == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /local/genbank/workspace/reads.spadescorr.k55/K55/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.k55/dataset.info) with K=55 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 0:00:00.013 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.013 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.963 76M / 76M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:01.349 84M / 84M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:02.124 104M / 104M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:03.717 136M / 136M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:06.779 208M / 208M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:12.910 348M / 348M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:29.088 564M / 564M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:57.980 616M / 616M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:55.898 620M / 620M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:04:06.055 872M / 876M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:08:46.305 956M / 956M INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:18:13.821 916M / 956M INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:36:33.515 696M / 956M INFO General (binary_converter.hpp : 93) 67108864 reads processed 0:56:29.397 636M / 956M INFO General (binary_converter.hpp : 117) 105822607 reads written 0:56:32.470 8M / 956M INFO General (read_converter.hpp : 87) Converting single reads 0:56:33.007 136M / 956M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:56:33.138 140M / 956M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:56:33.403 152M / 956M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:56:33.929 168M / 956M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:56:34.980 204M / 956M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:56:37.091 276M / 956M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:56:41.327 420M / 956M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:56:49.642 708M / 956M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:57:06.616 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:57:49.791 1G / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:59:16.458 1G / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed 1:02:13.230 1G / 1G INFO General (binary_converter.hpp : 93) 33554432 reads processed 1:08:19.910 1G / 1G INFO General (binary_converter.hpp : 93) 67108864 reads processed 1:16:14.182 3G / 3G INFO General (binary_converter.hpp : 117) 99317237 reads written 1:16:24.636 16M / 3G INFO General (read_converter.hpp : 95) Converting merged reads 1:16:25.100 144M / 3G INFO General (binary_converter.hpp : 117) 0 reads written 1:16:25.377 12M / 3G INFO General (construction.cpp : 111) Max read length 700 1:16:25.377 12M / 3G INFO General (construction.cpp : 117) Average read length 77.5334 1:16:25.377 12M / 3G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 1:16:25.383 12M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 1:16:25.390 8M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:16:25.390 8M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.34367 Gb 1:16:25.390 8M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 1:17:33.800 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 61269675 reads 1:18:31.622 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 137893934 reads 1:19:11.079 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 170443977 reads 1:20:24.038 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 195586316 reads 1:22:02.809 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 230837631 reads 1:23:34.267 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 278316078 reads 1:24:57.466 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 325216340 reads 1:26:20.401 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 365374475 reads 1:27:20.079 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 395157671 reads 1:28:24.263 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 447952737 reads 1:29:25.772 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 525128859 reads 1:30:27.905 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 598720122 reads 1:31:04.284 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 621924902 reads 1:31:04.284 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 1:31:10.421 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 621924902 reads 1:31:10.421 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:37:45.433 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1170278194 kmers in total. 1:37:45.433 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:41:36.334 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 1:41:36.338 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:41:36.338 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:41:36.341 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:41:36.341 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.34245 Gb 1:41:36.341 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 1:41:46.367 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 7469412 kmers 1:41:53.599 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 16778563 kmers 1:42:01.433 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26186767 kmers 1:42:10.715 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34675149 kmers 1:42:19.202 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 44007845 kmers 1:42:28.272 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 53304607 kmers 1:42:38.070 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 62720412 kmers 1:42:47.662 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 71216679 kmers 1:42:57.807 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 80578487 kmers 1:43:06.942 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 89870178 kmers 1:43:17.247 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 99281260 kmers 1:43:27.736 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 107783598 kmers 1:43:35.936 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 117149962 kmers 1:43:45.075 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 126445415 kmers 1:43:55.279 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 135865960 kmers 1:44:05.028 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 144362229 kmers 1:44:15.933 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 153720998 kmers 1:44:24.696 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 163028391 kmers 1:46:23.245 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 272737998 kmers 1:52:28.270 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 538155904 kmers 2:07:20.160 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1077335752 kmers 2:09:37.076 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 1170282290 kmers. 2:09:41.088 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 2:16:20.578 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1182731503 kmers in total. 2:16:20.578 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 2:20:09.449 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 2:22:01.639 704M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 2:25:14.966 704M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 548443480 bytes occupied (3.70967 bits per kmer). 2:25:17.413 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 2:26:25.322 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 2:26:25.335 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 2:26:25.593 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 2:28:12.364 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 58312382 sequences extracted 2:29:04.095 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 2:29:29.516 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 124 loops collected 2:31:13.102 20G / 26G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 2:31:13.102 20G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:31:13.102 20G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 2:32:18.659 21G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 542689780 bytes occupied (3.70982 bits per kmer). 2:32:25.988 25G / 26G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 2:37:05.364 25G / 26G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 2:37:34.585 25G / 26G INFO General (construction.cpp : 464) Processed 32000000 edges 2:37:57.395 25G / 26G INFO General (construction.cpp : 464) Processed 64000000 edges 2:38:19.843 25G / 26G INFO General (construction.cpp : 464) Processed 96000000 edges 2:38:33.448 25G / 26G INFO General (construction.cpp : 464) Processed 116623318 edges 2:38:49.224 19G / 26G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 2:38:50.193 19G / 26G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 212 2:38:50.212 19G / 26G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 213 2:38:50.212 19G / 26G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 2:38:50.212 19G / 26G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 213. Coverage mad: 48.3837 2:38:50.236 19G / 26G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 2:38:51.849 19G / 26G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 2:38:55.313 19G / 26G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 2:38:58.722 19G / 26G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 386.521. Fitted coverage std. dev: 36.9019 2:38:58.762 19G / 26G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 2:38:58.762 19G / 26G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 212 2:38:58.762 19G / 26G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 837906 2:38:58.762 19G / 26G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 2:38:58.762 19G / 26G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 212 2:38:58.762 19G / 26G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 2:38:58.762 19G / 26G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 2:38:58.762 19G / 26G INFO General (graph_pack.hpp : 101) Index refill 2:38:58.769 19G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 2:38:58.769 19G / 26G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 2:38:58.775 19G / 26G INFO General (file_limit.hpp : 32) Open file limit set to 4096 2:38:58.775 19G / 26G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.14258 Gb 2:38:58.775 19G / 26G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 2:42:01.766 36G / 37G INFO General (edge_index_builders.hpp : 77) Processed 89363993 edges 2:43:01.295 36G / 37G INFO General (edge_index_builders.hpp : 77) Processed 116623350 edges 2:43:01.295 36G / 37G INFO General (edge_index_builders.hpp : 82) Used 116623350 sequences. 2:43:08.467 19G / 37G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 2:46:01.670 19G / 37G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1170278194 kmers in total. 2:46:01.670 19G / 37G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 2:49:46.091 19G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 2:51:55.360 19G / 37G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 2:55:17.136 19G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 542676560 bytes occupied (3.70973 bits per kmer). 2:55:42.660 46G / 46G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 2:56:41.138 46G / 46G INFO General (edge_index.hpp : 92) Index refilled 2:56:41.172 46G / 46G INFO General (gap_closer.cpp : 159) Preparing shift maps 2:59:46.237 53G / 53G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 3:01:32.566 55G / 55G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 3:01:32.566 55G / 55G INFO General (gap_closer.cpp : 140) Merging paired indices 3:03:43.515 47G / 55G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 3:17:10.417 47G / 55G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 142275 gaps after checking 1458115 candidates 3:20:10.421 46G / 55G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 3:20:22.495 19G / 55G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 3:20:22.540 19G / 55G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 3:20:22.540 19G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 3:20:35.573 19G / 55G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 3:20:35.574 19G / 55G INFO StageManager (stage.cpp : 132) STAGE == Simplification 3:20:35.574 19G / 55G INFO General (simplification.cpp : 357) Graph simplification started 3:20:35.574 19G / 55G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 3:20:35.574 19G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 3:20:35.574 19G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 3:41:15.808 20G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20989839 times 3:41:15.808 20G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 3:58:26.540 23G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 825416 times 3:58:26.540 23G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:00:18.288 23G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 615486 times 4:00:18.288 23G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 4:00:18.288 23G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:00:31.989 23G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 115898 times 4:00:31.989 23G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:09.594 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 24345 times 4:01:09.594 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:12.121 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 14621 times 4:01:12.121 24G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 4:01:12.121 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:01:12.215 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 180 times 4:01:12.215 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:18.687 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2698 times 4:01:18.687 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:19.109 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3916 times 4:01:19.109 24G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 4:01:19.109 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:01:19.128 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 52 times 4:01:19.128 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:20.226 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 734 times 4:01:20.226 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:20.410 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1851 times 4:01:20.410 24G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 4:01:20.410 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:01:20.419 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 28 times 4:01:20.419 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:21.004 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 367 times 4:01:21.005 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:21.115 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1101 times 4:01:21.115 24G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 4:01:21.115 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:01:21.120 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 22 times 4:01:21.120 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:21.400 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 213 times 4:01:21.401 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:21.470 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 692 times 4:01:21.470 24G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 4:01:21.470 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:01:21.473 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 14 times 4:01:21.473 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:21.703 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 124 times 4:01:21.703 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:21.751 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 496 times 4:01:21.751 24G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 4:01:21.751 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:01:21.753 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 4:01:21.753 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:21.864 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 84 times 4:01:21.864 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:21.896 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 351 times 4:01:21.896 24G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 4:01:21.896 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:01:21.897 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times 4:01:21.897 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:21.954 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 60 times 4:01:21.954 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:21.980 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 255 times 4:01:21.980 24G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 4:01:21.980 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:01:21.981 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5 times 4:01:21.981 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:22.016 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 41 times 4:01:22.016 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:22.039 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 240 times 4:01:22.039 24G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 4:01:22.039 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:01:27.731 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1573 times 4:01:27.731 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:32.677 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 81 times 4:01:32.677 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:36.614 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 4:01:36.614 24G / 55G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 4:01:36.614 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:01:36.615 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 4:01:36.615 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:01:36.615 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 4:01:36.615 24G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 4:01:36.615 24G / 55G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 4:01:36.615 24G / 55G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 4:01:36.615 24G / 55G INFO General (graph_pack.hpp : 101) Index refill 4:01:36.668 24G / 55G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 4:01:36.668 24G / 55G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 4:01:36.674 24G / 55G INFO General (file_limit.hpp : 32) Open file limit set to 4096 4:01:36.674 24G / 55G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.0933 Gb 4:01:36.674 24G / 55G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 4:04:59.538 41G / 55G INFO General (edge_index_builders.hpp : 77) Processed 27769849 edges 4:04:59.539 41G / 55G INFO General (edge_index_builders.hpp : 82) Used 27769849 sequences. 4:05:05.160 24G / 55G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 4:07:43.440 24G / 55G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 682881511 kmers in total. 4:07:43.440 24G / 55G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 4:09:52.181 24G / 55G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 4:11:00.543 24G / 55G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 4:12:52.026 24G / 55G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 316661712 bytes occupied (3.70971 bits per kmer). 4:13:10.359 39G / 55G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 4:13:43.292 39G / 55G INFO General (edge_index.hpp : 92) Index refilled 4:13:43.389 39G / 55G INFO General (gap_closer.cpp : 159) Preparing shift maps 4:14:48.302 43G / 55G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 4:17:31.100 47G / 55G INFO General (gap_closer.cpp : 138) Used 105822607 paired reads 4:17:31.100 47G / 55G INFO General (gap_closer.cpp : 140) Merging paired indices 4:21:12.260 40G / 55G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 4:26:11.128 40G / 55G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 102968 gaps after checking 1883832 candidates 4:32:39.790 39G / 55G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 4:32:39.790 39G / 55G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 4:32:39.790 39G / 55G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 4:32:39.790 39G / 55G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 4:32:39.791 39G / 55G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 4:32:39.791 39G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:32:49.834 39G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 4:32:49.835 39G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:32:56.771 39G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 4:32:56.771 39G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 4:33:02.704 39G / 55G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 4:33:02.704 39G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 4:33:08.538 39G / 55G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 4:33:08.538 39G / 55G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 4:34:34.652 39G / 55G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 5:05:57.760 28G / 55G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 13629985 times 5:05:57.762 28G / 55G INFO General (simplification.cpp : 470) Counting average coverage 5:06:02.032 28G / 55G INFO General (simplification.cpp : 476) Average coverage = 18.5641 5:06:02.032 28G / 55G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly 5:06:02.032 28G / 55G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 5:06:02.032 28G / 55G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 103333469 kmers to process 5:10:46.534 28G / 55G INFO General (graph_pack.hpp : 111) Normalizing done 5:48:12.003 91G / 91G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 5:59:45.965 30G / 91G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 6:00:07.076 28G / 91G INFO General (mismatch_correction.cpp : 27) Corrected 639 nucleotides 6:00:07.079 28G / 91G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 6:00:07.079 28G / 91G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.spadescorr.k55//K55/assembly_graph_with_scaffolds.gfa 6:00:22.021 28G / 91G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k55//K55/before_rr.fasta 6:00:36.180 28G / 91G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.spadescorr.k55//K55/assembly_graph.fastg 6:02:24.531 28G / 91G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k55//K55/simplified_contigs.fasta 6:02:41.047 28G / 91G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k55//K55/intermediate_contigs.fasta 6:02:56.581 28G / 91G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 6:02:59.266 28G / 91G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 103378947 kmers to process 6:07:11.544 28G / 91G INFO General (graph_pack.hpp : 111) Normalizing done 6:07:12.986 28G / 91G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 3046 6:07:12.986 28G / 91G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 6:07:12.986 28G / 91G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 6:07:15.341 28G / 91G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 6:07:24.305 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 6:07:24.455 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 6:07:24.517 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 6:07:24.752 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 6:07:24.818 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 6:07:24.882 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 6:07:25.206 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 6:07:26.048 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 6:07:39.509 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 6:07:57.461 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 6:08:35.367 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 6:09:44.730 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 6:10:48.820 28G / 91G INFO General (sequence_mapper_notifier.h: 98) Total 105822607 reads processed 6:10:50.009 28G / 91G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 6:10:50.009 28G / 91G INFO General (pair_info_count.cpp : 213) 21075752 paired reads (19.9161% of all) aligned to long edges 6:10:50.246 28G / 91G INFO General (pair_info_count.cpp : 354) Insert size = 257.328, deviation = 65.8911, left quantile = 173, right quantile = 325, read length = 700 6:10:50.246 28G / 91G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 257.328 is very small compared to read length 700 6:10:50.478 28G / 91G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 6:10:50.709 28G / 91G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 6:10:58.134 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 6:10:58.169 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 6:10:58.192 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 6:10:58.208 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 6:10:58.217 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 6:10:58.286 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 6:10:58.446 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 6:10:58.739 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 6:11:11.185 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 6:11:26.186 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 6:12:03.989 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 6:13:10.262 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 6:14:07.122 28G / 91G INFO General (sequence_mapper_notifier.h: 98) Total 105822607 reads processed 6:14:07.124 28G / 91G INFO General (pair_info_count.cpp : 383) Mapping library #0 6:14:07.124 28G / 91G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 6:14:07.124 28G / 91G INFO General (pair_info_count.cpp : 289) Left insert size quantile 173, right insert size quantile 325, filtering threshold 2, rounding threshold 0 6:14:07.200 28G / 91G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 6:14:23.991 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 6:14:24.470 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 6:14:24.889 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 6:14:24.927 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 6:14:25.095 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 6:14:25.114 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 6:14:25.823 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 6:14:27.283 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 6:14:39.712 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 6:14:55.034 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 6:15:33.969 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads 6:16:41.006 28G / 91G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads 6:17:40.222 29G / 91G INFO General (sequence_mapper_notifier.h: 98) Total 105822607 reads processed 6:17:40.514 28G / 91G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 6:17:40.514 28G / 91G INFO General (distance_estimation.cpp : 173) Processing library #0 6:17:40.514 28G / 91G INFO General (distance_estimation.cpp : 149) Weight Filter Done 6:17:40.514 28G / 91G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 6:19:04.466 29G / 91G INFO General (distance_estimation.cpp : 34) Filtering info 6:19:04.467 29G / 91G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 21833652 6:19:30.321 29G / 91G INFO General (pair_info_filters.hpp : 263) Done filtering 6:19:30.321 29G / 91G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 6:19:32.267 29G / 91G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 6:19:32.267 29G / 91G INFO General (distance_estimation.cpp : 160) Improving paired information 6:21:24.220 29G / 91G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1267734; contradictional = 476 6:26:46.061 29G / 91G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 583471; contradictional = 80 6:26:46.061 29G / 91G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 6:26:46.062 29G / 91G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 6:28:08.187 29G / 91G INFO General (distance_estimation.cpp : 34) Filtering info 6:28:08.187 29G / 91G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 1492840 6:28:09.963 29G / 91G INFO General (pair_info_filters.hpp : 263) Done filtering 6:28:09.963 29G / 91G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 6:28:21.865 28G / 91G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 6:28:21.865 28G / 91G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 6:28:21.865 28G / 91G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 6:28:25.772 29G / 91G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 6:28:25.774 29G / 91G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 18.5641 6:28:25.904 29G / 91G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 18.5641 6:28:26.622 29G / 91G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 6:28:26.622 29G / 91G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 6:28:26.622 29G / 91G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 6:28:26.622 29G / 91G INFO General (launcher.cpp : 420) Total number of extenders is 3 6:28:26.622 29G / 91G INFO General (path_extender.hpp : 885) Processed 0 paths from 145246 (0%) 6:28:27.020 29G / 91G INFO General (path_extender.hpp : 883) Processed 128 paths from 145246 (0%) 6:28:27.303 29G / 91G INFO General (path_extender.hpp : 883) Processed 256 paths from 145246 (0%) 6:28:27.940 29G / 91G INFO General (path_extender.hpp : 883) Processed 512 paths from 145246 (0%) 6:28:29.581 29G / 91G INFO General (path_extender.hpp : 883) Processed 1024 paths from 145246 (0%) 6:28:32.924 29G / 91G INFO General (path_extender.hpp : 883) Processed 2048 paths from 145246 (1%) 6:28:38.139 29G / 91G INFO General (path_extender.hpp : 883) Processed 4096 paths from 145246 (2%) 6:28:48.828 29G / 91G INFO General (path_extender.hpp : 883) Processed 8192 paths from 145246 (5%) 6:29:03.695 29G / 91G INFO General (path_extender.hpp : 885) Processed 14525 paths from 145246 (10%) 6:29:08.202 29G / 91G INFO General (path_extender.hpp : 883) Processed 16384 paths from 145246 (11%) 6:29:34.973 29G / 91G INFO General (path_extender.hpp : 885) Processed 29050 paths from 145246 (20%) 6:29:42.382 29G / 91G INFO General (path_extender.hpp : 883) Processed 32768 paths from 145246 (22%) 6:30:02.582 29G / 91G INFO General (path_extender.hpp : 885) Processed 43575 paths from 145246 (30%) 6:30:25.723 29G / 91G INFO General (path_extender.hpp : 885) Processed 58100 paths from 145246 (40%) 6:30:33.608 29G / 91G INFO General (path_extender.hpp : 883) Processed 65536 paths from 145246 (45%) 6:30:40.212 29G / 91G INFO General (path_extender.hpp : 885) Processed 72625 paths from 145246 (50%) 6:30:52.258 30G / 91G INFO General (path_extender.hpp : 885) Processed 87150 paths from 145246 (60%) 6:31:01.137 30G / 91G INFO General (path_extender.hpp : 885) Processed 101675 paths from 145246 (70%) 6:31:08.413 30G / 91G INFO General (path_extender.hpp : 885) Processed 116200 paths from 145246 (80%) 6:31:21.978 30G / 91G INFO General (path_extender.hpp : 885) Processed 130725 paths from 145246 (90%) 6:31:22.034 30G / 91G INFO General (path_extender.hpp : 883) Processed 131072 paths from 145246 (90%) 6:31:23.547 30G / 91G INFO General (launcher.cpp : 234) Finalizing paths 6:31:23.547 30G / 91G INFO General (launcher.cpp : 236) Deduplicating paths 6:33:28.652 30G / 91G INFO General (launcher.cpp : 240) Paths deduplicated 6:33:28.652 30G / 91G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 6:33:28.652 30G / 91G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 6:33:29.372 30G / 91G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 6:33:29.372 30G / 91G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 6:37:27.040 30G / 91G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 6:41:25.067 30G / 91G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 6:41:26.901 30G / 91G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 6:41:52.873 30G / 91G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 6:41:56.038 30G / 91G INFO General (launcher.cpp : 257) Paths finalized 6:41:56.038 30G / 91G INFO General (launcher.cpp : 427) Closing gaps in paths 6:41:58.060 30G / 91G INFO General (launcher.cpp : 455) Gap closing completed 6:41:58.564 30G / 91G INFO General (launcher.cpp : 286) Traversing tandem repeats 6:42:01.766 30G / 91G INFO General (launcher.cpp : 296) Traversed 0 loops 6:42:01.766 30G / 91G INFO General (launcher.cpp : 234) Finalizing paths 6:42:01.766 30G / 91G INFO General (launcher.cpp : 236) Deduplicating paths 6:42:01.978 30G / 91G INFO General (launcher.cpp : 240) Paths deduplicated 6:42:01.978 30G / 91G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 6:42:01.978 30G / 91G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 6:42:02.336 30G / 91G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 6:42:02.336 30G / 91G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 6:42:02.746 30G / 91G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 6:42:03.213 30G / 91G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 6:42:03.256 30G / 91G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 6:42:03.453 30G / 91G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 6:42:04.455 30G / 91G INFO General (launcher.cpp : 257) Paths finalized 6:42:05.799 30G / 91G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 6:42:11.217 29G / 91G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 6:42:11.217 29G / 91G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.spadescorr.k55//K55/assembly_graph_with_scaffolds.gfa 6:42:21.127 29G / 91G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.spadescorr.k55//K55/before_rr.fasta 6:42:34.998 29G / 91G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.spadescorr.k55//K55/assembly_graph.fastg 6:43:19.571 29G / 91G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.spadescorr.k55//K55/final_contigs.paths 6:43:34.094 29G / 91G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.spadescorr.k55//K55/scaffolds.paths 6:43:47.001 29G / 91G INFO General (launch.hpp : 149) SPAdes finished 6:46:46.577 196M / 91G INFO General (main.cpp : 109) Assembling time: 6 hours 46 minutes 46 seconds ===== Assembling finished. Used k-mer sizes: 55 * Assembled contigs are in /local/genbank/workspace/reads.spadescorr.k55/contigs.fasta * Assembled scaffolds are in /local/genbank/workspace/reads.spadescorr.k55/scaffolds.fasta * Assembly graph is in /local/genbank/workspace/reads.spadescorr.k55/assembly_graph.fastg * Assembly graph in GFA format is in /local/genbank/workspace/reads.spadescorr.k55/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /local/genbank/workspace/reads.spadescorr.k55/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /local/genbank/workspace/reads.spadescorr.k55/scaffolds.paths ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 2:38:50.212 19G / 26G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable * 2:38:58.762 19G / 26G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 212 * 5:06:02.032 28G / 55G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly * 6:10:50.246 28G / 91G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 257.328 is very small compared to read length 700 ======= Warnings saved to /local/genbank/workspace/reads.spadescorr.k55/warnings.log SPAdes log can be found here: /local/genbank/workspace/reads.spadescorr.k55/spades.log Thank you for using SPAdes!