Command line: /home/psgendb/BIRCHDEV/bin-linux-x86_64/spades.py -1 /local/genbank/workspace/reads.all/AB2kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq -2 /local/genbank/workspace/reads.all/AB2kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq -1 /local/genbank/workspace/reads.all/AB4kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq -2 /local/genbank/workspace/reads.all/AB4kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq -1 /local/genbank/workspace/reads.all/20090202_7_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/20090202_7_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/20090202_8_1_valid_1P.fq.corrected.fq -2 /local/genbank/workspace/reads.all/20090202_8_2_valid_2P.fq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae6.2GB_6_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae6.2GB_6_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae6.2GB_7_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae6.2GB_7_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae6.2GB_8_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae6.2GB_8_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae7.2GB_6_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae7.2GB_6_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae7.2GB_7_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae7.2GB_7_2_2P.fastq.corrected.fq -1 /local/genbank/workspace/reads.all/Algae7.2GB_8_1_1P.fastq.corrected.fq -2 /local/genbank/workspace/reads.all/Algae7.2GB_8_2_2P.fastq.corrected.fq -s /local/genbank/workspace/reads.all/454.corrected.fq -s /local/genbank/workspace/reads.all/2008SE.fq -s /local/genbank/workspace/reads.all/20090202.pollux.unpaired.fq -s /local/genbank/workspace/reads.all/367GB.fq -s /local/genbank/workspace/reads.all/AB4kbUnpaired.fq --only-assembler -k 55 -m 63 -t 32 -o /local/genbank/workspace/reads.all/spades2 System information: SPAdes version: 3.13.0 Python version: 2.7.5 OS: Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-redhat-7.9-Maipo Output dir: /local/genbank/workspace/reads.all/spades2 Mode: ONLY assembling (without read error correction) Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/local/genbank/workspace/reads.all/AB2kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq', '/local/genbank/workspace/reads.all/AB4kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq', '/local/genbank/workspace/reads.all/20090202_7_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/20090202_8_1_valid_1P.fq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_6_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_7_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_8_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_6_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_7_1_1P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_8_1_1P.fastq.corrected.fq'] right reads: ['/local/genbank/workspace/reads.all/AB2kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq', '/local/genbank/workspace/reads.all/AB4kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq', '/local/genbank/workspace/reads.all/20090202_7_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/20090202_8_2_valid_2P.fq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_6_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_7_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae6.2GB_8_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_6_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_7_2_2P.fastq.corrected.fq', '/local/genbank/workspace/reads.all/Algae7.2GB_8_2_2P.fastq.corrected.fq'] interlaced reads: not specified single reads: ['/local/genbank/workspace/reads.all/454.corrected.fq', '/local/genbank/workspace/reads.all/2008SE.fq', '/local/genbank/workspace/reads.all/20090202.pollux.unpaired.fq', '/local/genbank/workspace/reads.all/367GB.fq', '/local/genbank/workspace/reads.all/AB4kbUnpaired.fq'] merged reads: not specified Assembly parameters: k: [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.all/spades2/tmp Threads: 32 Memory limit (in Gb): 63 ======= SPAdes pipeline started. Log can be found here: /local/genbank/workspace/reads.all/spades2/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.all/spades2/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 63 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/local/genbank/workspace/reads.all/spades2/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.083 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.083 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.533 76M / 76M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.719 88M / 88M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:01.089 108M / 108M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:01.829 148M / 148M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:03.316 228M / 228M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:06.313 388M / 388M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:15.398 644M / 644M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:31.194 648M / 648M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:01.695 684M / 684M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:02:06.492 708M / 708M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:04:15.774 728M / 728M INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:08:02.671 652M / 856M INFO General (binary_converter.hpp : 93) 33554432 reads processed 0:08:24.564 604M / 856M INFO General (binary_converter.hpp : 117) 35067264 reads written 0:08:26.362 4M / 856M INFO General (read_converter.hpp : 87) Converting single reads 0:08:26.758 144M / 856M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:08:26.995 156M / 856M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:08:27.488 184M / 856M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:08:28.476 240M / 856M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:08:30.310 340M / 856M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:08:33.165 508M / 856M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:08:39.934 904M / 904M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:08:47.278 1G / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:08:56.764 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:09:24.289 1G / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:10:12.573 1G / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed 0:10:58.106 960M / 1G INFO General (binary_converter.hpp : 117) 22655284 reads written 0:11:00.274 8M / 1G INFO General (read_converter.hpp : 95) Converting merged reads 0:11:00.495 136M / 1G INFO General (binary_converter.hpp : 117) 0 reads written 0:11:02.465 4M / 1G INFO General (construction.cpp : 111) Max read length 581 0:11:02.465 4M / 1G INFO General (construction.cpp : 117) Average read length 84.7984 0:11:02.465 4M / 1G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:11:02.468 4M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while. 0:11:02.470 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:11:02.470 4M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.656209 Gb 0:11:02.470 4M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768 0:11:27.286 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 11599147 reads 0:11:37.412 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 22273580 reads 0:11:51.066 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 40330742 reads 0:12:09.470 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 48615428 reads 0:12:49.657 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 73931661 reads 0:13:30.103 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 98524888 reads 0:13:57.833 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 113963092 reads 0:14:27.175 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 139313362 reads 0:14:53.626 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 176206074 reads 0:15:06.533 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 185579624 reads 0:15:06.533 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:15:09.554 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 185579624 reads 0:15:09.554 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:16:43.471 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 591092279 kmers in total. 0:16:43.471 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:18:25.796 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:18:25.798 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:18:25.798 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:18:25.800 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:18:25.800 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.654948 Gb 0:18:25.800 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:18:31.901 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8074204 kmers 0:18:37.128 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 16690809 kmers 0:18:42.082 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26511901 kmers 0:18:46.965 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 35133676 kmers 0:18:51.952 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 44968772 kmers 0:18:56.948 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 53589956 kmers 0:19:02.057 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 63445580 kmers 0:19:07.195 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 72069532 kmers 0:19:12.222 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 81922214 kmers 0:19:17.148 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 90532006 kmers 0:19:22.191 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 100400594 kmers 0:19:27.408 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 109020647 kmers 0:19:32.542 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 118867619 kmers 0:19:37.518 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 127485545 kmers 0:19:42.904 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 137326771 kmers 0:19:47.809 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 145945812 kmers 0:19:52.980 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 155802044 kmers 0:19:57.927 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 164425582 kmers 0:20:58.763 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 275243199 kmers 0:23:25.366 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 543713135 kmers 0:23:52.888 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 591094327 kmers. 0:23:55.046 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:26:45.401 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 596923171 kmers in total. 0:26:45.401 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:28:27.987 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:29:08.694 452M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:30:46.387 452M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 276803160 bytes occupied (3.70973 bits per kmer). 0:30:47.125 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:31:19.033 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:31:19.040 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:31:19.222 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:32:09.168 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 26533615 sequences extracted 0:32:35.015 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:32:47.322 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 168 loops collected 0:33:20.547 9G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:33:20.548 9G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:33:20.548 9G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:33:43.891 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 274129740 bytes occupied (3.71014 bits per kmer). 0:33:44.970 12G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:35:00.640 12G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:35:22.628 12G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges 0:35:34.638 12G / 18G INFO General (construction.cpp : 464) Processed 53066458 edges 0:35:38.909 8G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:35:39.556 8G / 18G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 134 0:35:39.580 8G / 18G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 135 0:35:39.580 8G / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable 0:35:39.580 8G / 18G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 135. Coverage mad: 38.5191 0:35:39.608 8G / 18G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:35:40.147 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:35:41.436 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:35:45.357 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:35:53.421 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:36:10.459 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:36:40.402 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:37:26.595 8G / 18G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 0:37:28.029 8G / 18G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 12.7111. Fitted coverage std. dev: 5.37058 0:37:28.029 8G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 6 0:37:28.039 8G / 18G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.915998 0:37:28.039 8G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 6 0:37:28.039 8G / 18G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 100691261 0:37:28.039 8G / 18G INFO General (genomic_info_filler.cpp : 114) Failed to estimate mean coverage 0:37:28.039 8G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 6 0:37:28.039 8G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:37:28.039 8G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:37:28.039 8G / 18G INFO General (graph_pack.hpp : 101) Index refill 0:37:28.046 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:37:28.046 8G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 0:37:28.048 8G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 4096 0:37:28.048 8G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.563721 Gb 0:37:28.048 8G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 0:39:14.906 26G / 27G INFO General (edge_index_builders.hpp : 77) Processed 53066458 edges 0:39:14.906 26G / 27G INFO General (edge_index_builders.hpp : 82) Used 53066458 sequences. 0:39:18.660 8G / 27G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:40:45.405 8G / 27G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 591092279 kmers in total. 0:40:45.405 8G / 27G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:42:27.065 8G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:43:13.374 9G / 27G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:44:43.521 9G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 274102582 bytes occupied (3.70978 bits per kmer). 0:44:54.479 22G / 27G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:45:21.986 22G / 27G INFO General (edge_index.hpp : 92) Index refilled 0:45:22.009 22G / 27G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:46:47.183 26G / 27G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:47:25.806 27G / 27G INFO General (gap_closer.cpp : 138) Used 35067264 paired reads 0:47:25.806 27G / 27G INFO General (gap_closer.cpp : 140) Merging paired indices 0:48:25.805 23G / 27G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:52:55.716 23G / 27G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 138258 gaps after checking 1746058 candidates 0:54:29.806 22G / 27G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:54:33.126 8G / 27G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:54:33.126 8G / 27G INFO General (simplification.cpp : 68) Most init cleaning disabled since detected mean 0 was less than activation coverage 10 0:54:33.126 8G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:54:36.950 8G / 27G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:54:36.950 8G / 27G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:54:36.950 8G / 27G INFO General (simplification.cpp : 357) Graph simplification started 0:54:36.953 8G / 27G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:54:36.953 8G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:54:36.953 8G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:00:28.735 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 10320731 times 1:00:28.735 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:23.193 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 88397 times 1:01:23.193 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:25.857 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 136 times 1:01:25.857 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 1:01:25.858 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:26.220 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3666 times 1:01:26.220 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:26.491 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 172 times 1:01:26.491 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:30.207 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 43072 times 1:01:30.207 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 1:01:30.207 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:31.622 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 25404 times 1:01:31.622 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:36.903 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5110 times 1:01:36.903 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:38.824 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 15012 times 1:01:38.824 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 1:01:38.824 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:39.338 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6803 times 1:01:39.338 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:42.246 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2398 times 1:01:42.246 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:44.493 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 18915 times 1:01:44.493 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 1:01:44.493 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:45.023 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7708 times 1:01:45.023 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:48.145 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3016 times 1:01:48.145 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:49.502 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11907 times 1:01:49.502 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 1:01:49.502 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:49.815 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4117 times 1:01:49.815 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:53.026 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1967 times 1:01:53.026 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:53.813 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5967 times 1:01:53.813 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 1:01:53.813 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:53.967 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1760 times 1:01:53.967 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:55.376 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1178 times 1:01:55.376 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:55.998 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6098 times 1:01:55.998 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 1:01:55.998 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:56.128 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1656 times 1:01:56.128 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:57.577 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1162 times 1:01:57.577 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:57.996 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4275 times 1:01:57.996 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 1:01:57.996 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:58.065 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 972 times 1:01:58.065 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:01:59.176 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 910 times 1:01:59.176 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:01:59.595 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4144 times 1:01:59.595 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 1:01:59.595 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:01:59.658 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 880 times 1:01:59.658 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:02:00.555 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 796 times 1:02:00.555 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:02:00.890 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3457 times 1:02:00.890 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 1:02:00.890 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:02:03.453 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3473 times 1:02:03.453 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:02:06.272 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 920 times 1:02:06.272 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:02:07.933 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 14 times 1:02:07.933 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 1:02:07.933 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:02:07.939 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 30 times 1:02:07.939 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:02:07.944 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4 times 1:02:07.944 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:02:07.944 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:02:07.944 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13 1:02:07.944 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:02:07.944 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:02:07.944 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:02:07.944 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:02:07.944 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 1:02:07.944 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 1:02:07.944 9G / 27G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 1:02:07.944 9G / 27G INFO General (graph_pack.hpp : 101) Index refill 1:02:07.950 9G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 1:02:07.950 9G / 27G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while. 1:02:07.952 9G / 27G INFO General (file_limit.hpp : 32) Open file limit set to 4096 1:02:07.952 9G / 27G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.553507 Gb 1:02:07.952 9G / 27G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536 1:03:17.598 27G / 27G INFO General (edge_index_builders.hpp : 77) Processed 12141693 edges 1:03:17.599 27G / 27G INFO General (edge_index_builders.hpp : 82) Used 12141693 sequences. 1:03:20.676 9G / 27G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 1:04:18.103 9G / 27G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 387820909 kmers in total. 1:04:18.103 9G / 27G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 1:05:24.655 9G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 1:05:47.866 10G / 27G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 1:06:52.289 10G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 179845488 bytes occupied (3.70987 bits per kmer). 1:07:01.664 18G / 27G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 1:07:16.846 18G / 27G INFO General (edge_index.hpp : 92) Index refilled 1:07:16.871 18G / 27G INFO General (gap_closer.cpp : 159) Preparing shift maps 1:07:48.129 20G / 27G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 1:08:39.590 24G / 27G INFO General (gap_closer.cpp : 138) Used 35067264 paired reads 1:08:39.590 24G / 27G INFO General (gap_closer.cpp : 140) Merging paired indices 1:10:28.774 19G / 27G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 1:12:19.460 19G / 27G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 126434 gaps after checking 1842152 candidates 1:15:16.503 18G / 27G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 1:15:16.503 18G / 27G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 1:15:16.503 18G / 27G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 1:15:16.503 18G / 27G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 1:15:16.503 18G / 27G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:15:16.503 18G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:15:19.587 18G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 57 times 1:15:19.587 18G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:15:21.634 18G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 1:15:21.634 18G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:15:23.467 18G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:15:23.467 18G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:15:25.452 18G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 1:15:25.452 18G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 1:15:25.452 18G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 1:15:25.452 18G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 1:15:25.452 18G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 1:15:25.452 18G / 27G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 1:15:42.663 18G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 1:23:36.215 13G / 27G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 5749028 times 1:23:36.216 13G / 27G INFO General (simplification.cpp : 470) Counting average coverage 1:23:36.539 13G / 27G INFO General (simplification.cpp : 476) Average coverage = 15.4194 1:23:36.539 13G / 27G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 1:23:36.539 13G / 27G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 13143987 kmers to process 1:23:51.701 13G / 27G INFO General (graph_pack.hpp : 111) Normalizing done 1:28:04.095 18G / 27G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 1:28:32.755 13G / 27G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 1:28:33.531 13G / 27G INFO General (mismatch_correction.cpp : 27) Corrected 346 nucleotides 1:28:33.532 13G / 27G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:28:33.532 13G / 27G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all/spades2//K55/assembly_graph_with_scaffolds.gfa 1:28:37.007 13G / 27G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades2//K55/before_rr.fasta 1:28:42.739 13G / 27G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all/spades2//K55/assembly_graph.fastg 1:28:58.723 13G / 27G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades2//K55/simplified_contigs.fasta 1:29:05.225 13G / 27G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades2//K55/intermediate_contigs.fasta 1:29:10.202 13G / 27G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 1:29:12.076 13G / 27G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 13171955 kmers to process 1:29:29.256 13G / 27G INFO General (graph_pack.hpp : 111) Normalizing done 1:29:30.180 13G / 27G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 1326 1:29:30.180 13G / 27G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 1:29:30.180 13G / 27G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 1:29:30.520 13G / 27G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:29:45.343 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 1:29:45.409 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 1:29:45.477 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 1:29:45.546 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 1:29:46.431 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 1:29:46.494 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 1:29:47.748 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 1:29:48.407 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 1:30:03.327 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 1:30:25.715 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 1:30:51.502 13G / 27G INFO General (sequence_mapper_notifier.h: 98) Total 35067264 reads processed 1:30:52.190 13G / 27G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 1:30:52.190 13G / 27G INFO General (pair_info_count.cpp : 213) 3059099 paired reads (8.72352% of all) aligned to long edges 1:30:52.197 13G / 27G INFO General (pair_info_count.cpp : 354) Insert size = 251.258, deviation = 74.2827, left quantile = 152, right quantile = 329, read length = 581 1:30:52.197 13G / 27G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 251.258 is very small compared to read length 581 1:30:52.270 13G / 27G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 1:30:52.316 13G / 27G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:31:07.307 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 1:31:07.471 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 1:31:07.496 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 1:31:07.607 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 1:31:07.709 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 1:31:07.810 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 1:31:08.162 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 1:31:08.494 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 1:31:23.094 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 1:31:45.829 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 1:32:10.908 13G / 27G INFO General (sequence_mapper_notifier.h: 98) Total 35067264 reads processed 1:32:10.909 13G / 27G INFO General (pair_info_count.cpp : 383) Mapping library #0 1:32:10.909 13G / 27G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 1:32:10.909 13G / 27G INFO General (pair_info_count.cpp : 289) Left insert size quantile 152, right insert size quantile 329, filtering threshold 2, rounding threshold 0 1:32:10.970 13G / 27G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 1:32:27.102 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 1:32:27.190 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 1:32:27.321 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 1:32:27.349 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 1:32:27.393 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 1:32:27.421 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 1:32:27.546 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 1:32:27.690 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 1:32:42.411 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads 1:33:16.759 13G / 27G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads 1:34:03.076 14G / 27G INFO General (sequence_mapper_notifier.h: 98) Total 35067264 reads processed 1:34:03.230 13G / 27G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 1:34:03.230 13G / 27G INFO General (distance_estimation.cpp : 173) Processing library #0 1:34:03.230 13G / 27G INFO General (distance_estimation.cpp : 149) Weight Filter Done 1:34:03.231 13G / 27G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 1:38:19.362 14G / 27G INFO General (distance_estimation.cpp : 34) Filtering info 1:38:19.363 14G / 27G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 60307186 1:39:04.043 14G / 27G INFO General (pair_info_filters.hpp : 263) Done filtering 1:39:04.044 14G / 27G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 1:39:08.384 14G / 27G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 1:39:08.384 14G / 27G INFO General (distance_estimation.cpp : 160) Improving paired information 1:40:04.010 14G / 27G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 3670008; contradictional = 42 1:41:50.352 14G / 27G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1019858; contradictional = 2 1:41:50.352 14G / 27G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 1:41:50.352 14G / 27G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 1:45:50.873 14G / 27G INFO General (distance_estimation.cpp : 34) Filtering info 1:45:50.873 14G / 27G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2712996 1:45:52.919 15G / 27G INFO General (pair_info_filters.hpp : 263) Done filtering 1:45:52.919 14G / 27G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 1:46:02.232 14G / 27G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 1:46:02.232 14G / 27G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 1:46:02.232 14G / 27G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 1:46:04.683 15G / 27G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 1:46:04.684 15G / 27G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 15.4194 1:46:04.777 15G / 27G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 15.4194 1:46:05.276 15G / 27G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 1:46:05.276 15G / 27G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 1:46:05.276 15G / 27G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 1:46:05.276 15G / 27G INFO General (launcher.cpp : 420) Total number of extenders is 3 1:46:05.276 15G / 27G INFO General (path_extender.hpp : 885) Processed 0 paths from 188464 (0%) 1:46:05.426 15G / 27G INFO General (path_extender.hpp : 883) Processed 128 paths from 188464 (0%) 1:46:05.554 15G / 27G INFO General (path_extender.hpp : 883) Processed 256 paths from 188464 (0%) 1:46:05.775 15G / 27G INFO General (path_extender.hpp : 883) Processed 512 paths from 188464 (0%) 1:46:06.294 15G / 27G INFO General (path_extender.hpp : 883) Processed 1024 paths from 188464 (0%) 1:46:07.123 15G / 27G INFO General (path_extender.hpp : 883) Processed 2048 paths from 188464 (1%) 1:46:08.549 15G / 27G INFO General (path_extender.hpp : 883) Processed 4096 paths from 188464 (2%) 1:46:11.189 15G / 27G INFO General (path_extender.hpp : 883) Processed 8192 paths from 188464 (4%) 1:46:15.072 15G / 27G INFO General (path_extender.hpp : 883) Processed 16384 paths from 188464 (8%) 1:46:16.191 15G / 27G INFO General (path_extender.hpp : 885) Processed 18847 paths from 188464 (10%) 1:46:21.333 15G / 27G INFO General (path_extender.hpp : 883) Processed 32768 paths from 188464 (17%) 1:46:22.891 15G / 27G INFO General (path_extender.hpp : 885) Processed 37694 paths from 188464 (20%) 1:46:27.633 15G / 27G INFO General (path_extender.hpp : 885) Processed 56541 paths from 188464 (30%) 1:46:29.488 15G / 27G INFO General (path_extender.hpp : 883) Processed 65536 paths from 188464 (34%) 1:46:31.228 15G / 27G INFO General (path_extender.hpp : 885) Processed 75388 paths from 188464 (40%) 1:46:51.711 15G / 27G INFO General (path_extender.hpp : 885) Processed 94235 paths from 188464 (50%) 1:47:44.849 15G / 27G INFO General (path_extender.hpp : 885) Processed 113082 paths from 188464 (60%) 1:48:11.762 16G / 27G INFO General (path_extender.hpp : 883) Processed 131072 paths from 188464 (69%) 1:48:12.691 16G / 27G INFO General (path_extender.hpp : 885) Processed 131929 paths from 188464 (70%) 1:48:30.733 16G / 27G INFO General (path_extender.hpp : 885) Processed 150776 paths from 188464 (80%) 1:48:42.121 16G / 27G INFO General (path_extender.hpp : 885) Processed 169623 paths from 188464 (90%) 1:48:49.541 16G / 27G INFO General (launcher.cpp : 234) Finalizing paths 1:48:49.541 16G / 27G INFO General (launcher.cpp : 236) Deduplicating paths 1:48:53.533 16G / 27G INFO General (launcher.cpp : 240) Paths deduplicated 1:48:53.533 16G / 27G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 1:48:53.533 16G / 27G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 1:48:53.944 16G / 27G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 1:48:53.944 16G / 27G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 1:48:54.765 16G / 27G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 1:48:55.565 16G / 27G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 1:48:55.704 16G / 27G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 1:48:55.944 16G / 27G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 1:48:57.965 16G / 27G INFO General (launcher.cpp : 257) Paths finalized 1:48:57.965 16G / 27G INFO General (launcher.cpp : 427) Closing gaps in paths 1:48:59.511 16G / 27G INFO General (launcher.cpp : 455) Gap closing completed 1:48:59.871 16G / 27G INFO General (launcher.cpp : 286) Traversing tandem repeats 1:49:02.420 16G / 27G INFO General (launcher.cpp : 296) Traversed 25 loops 1:49:02.420 16G / 27G INFO General (launcher.cpp : 234) Finalizing paths 1:49:02.420 16G / 27G INFO General (launcher.cpp : 236) Deduplicating paths 1:49:02.579 16G / 27G INFO General (launcher.cpp : 240) Paths deduplicated 1:49:02.579 16G / 27G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 1:49:02.579 16G / 27G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 1:49:02.859 16G / 27G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 1:49:02.859 16G / 27G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 1:49:03.177 16G / 27G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 1:49:03.545 16G / 27G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 1:49:03.575 16G / 27G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 1:49:03.735 16G / 27G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 1:49:04.509 16G / 27G INFO General (launcher.cpp : 257) Paths finalized 1:49:05.129 16G / 27G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 1:49:08.700 15G / 27G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 1:49:08.700 15G / 27G INFO General (contig_output_stage.cpp : 40) Writing GFA to /local/genbank/workspace/reads.all/spades2//K55/assembly_graph_with_scaffolds.gfa 1:49:12.066 15G / 27G INFO General (contig_output.hpp : 22) Outputting contigs to /local/genbank/workspace/reads.all/spades2//K55/before_rr.fasta 1:49:17.052 15G / 27G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /local/genbank/workspace/reads.all/spades2//K55/assembly_graph.fastg 1:49:33.656 15G / 27G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.all/spades2//K55/final_contigs.paths 1:49:41.452 15G / 27G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /local/genbank/workspace/reads.all/spades2//K55/scaffolds.paths 1:49:48.926 15G / 27G INFO General (launch.hpp : 149) SPAdes finished 1:50:21.100 148M / 27G INFO General (main.cpp : 109) Assembling time: 1 hours 50 minutes 21 seconds ===== Assembling finished. Used k-mer sizes: 55 * Assembled contigs are in /local/genbank/workspace/reads.all/spades2/contigs.fasta * Assembled scaffolds are in /local/genbank/workspace/reads.all/spades2/scaffolds.fasta * Assembly graph is in /local/genbank/workspace/reads.all/spades2/assembly_graph.fastg * Assembly graph in GFA format is in /local/genbank/workspace/reads.all/spades2/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /local/genbank/workspace/reads.all/spades2/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /local/genbank/workspace/reads.all/spades2/scaffolds.paths ======= SPAdes pipeline finished WITH WARNINGS! === Error correction and assembling warnings: * 0:35:39.580 8G / 18G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable * 0:37:28.029 8G / 18G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 6 * 0:37:28.039 8G / 18G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 6 * 1:30:52.197 13G / 27G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 251.258 is very small compared to read length 581 ======= Warnings saved to /local/genbank/workspace/reads.all/spades2/warnings.log SPAdes log can be found here: /local/genbank/workspace/reads.all/spades2/spades.log Thank you for using SPAdes!