Command line: /SPAdes-3.15.2-Linux/bin/rnaspades.py -t 8 -m 120 -o /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades --12 /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/reads.input.fastq.gz System information: SPAdes version: 3.15.2 Python version: 3.9.16 OS: Linux-5.14.21-150400.24.81_12.0.87-cray_shasta_c-x86_64-with-glibc2.34 Output dir: /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades Debug mode is turned OFF Dataset parameters: RNA-seq mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: not specified right reads: not specified interlaced reads: ['/pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/reads.input.fastq.gz'] single reads: not specified merged reads: not specified Assembly parameters: k: automatic selection based on read length 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: /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/tmp Threads: 8 Memory limit (in Gb): 120 ======= SPAdes pipeline started. Log can be found here: /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/spades.log /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/reads.input.fastq.gz: max reads length: 150 Reads length: 150 K values to be used: [49, 73] ===== Before start started. ===== Preprocess reads started. ===== Preprocess reads finished. ===== Assembling started. ===== K49 started. == Running: /SPAdes-3.15.2-Linux/bin/spades-core /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K49/configs/config.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K49/configs/mda_mode.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K49/configs/rna_mode.info 0:00:00.000 1M / 18M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K49/configs/config.info 0:00:00.013 1M / 18M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K49/configs/mda_mode.info 0:00:00.013 1M / 18M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K49/configs/rna_mode.info 0:00:00.013 1M / 18M INFO General (memory_limit.cpp : 48) Memory limit set to 120 Gb 0:00:00.013 1M / 18M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.2, git revision aab988a9b4986906b38396da7233bb1ee02982f2 0:00:00.013 1M / 18M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.013 1M / 18M INFO General (main.cpp : 109) Assembling dataset (/pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/dataset.info) with K=49 0:00:00.013 1M / 18M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 8 0:00:00.013 1M / 18M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.013 1M / 18M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.013 1M / 18M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.013 1M / 18M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.013 1M / 18M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.013 1M / 18M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:00.013 1M / 18M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.015 1M / 18M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.015 1M / 18M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.397 14M / 37M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:00.406 14M / 40M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:00.570 14M / 61M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:00.761 14M / 76M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:01.256 14M / 122M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:02.106 14M / 160M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:00:03.803 14M / 174M INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:00:07.019 14M / 196M INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:00:13.403 14M / 204M INFO General (binary_converter.cpp : 96) 4194304 reads processed 0:00:26.199 14M / 204M INFO General (binary_converter.cpp : 96) 8388608 reads processed 0:00:53.198 14M / 216M INFO General (binary_converter.cpp : 96) 16777216 reads processed 0:01:53.006 14M / 267M INFO General (binary_converter.cpp : 111) 33101602 reads written 0:01:53.006 7M / 267M INFO General (read_converter.cpp : 81) Converting single reads 0:01:53.008 11M / 267M INFO General (binary_converter.cpp : 111) 0 reads written 0:01:53.008 7M / 267M INFO General (read_converter.cpp : 87) Converting merged reads 0:01:53.009 11M / 267M INFO General (binary_converter.cpp : 111) 0 reads written 0:01:53.024 1M / 267M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:01:53.027 1M / 267M INFO General (construction.cpp : 153) Max read length 150 0:01:53.027 1M / 267M INFO General (construction.cpp : 159) Average read length 149.255 0:01:53.027 1M / 267M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:01:53.030 1M / 267M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:01:53.030 1M / 267M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:01:53.030 1M / 267M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:01:53.030 1M / 267M INFO General (kmer_splitter.hpp : 101) Using cell size of 419430 0:01:57.538 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 3568420 reads 0:02:02.170 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 7245428 reads 0:02:06.805 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 11073401 reads 0:02:11.397 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 14838461 reads 0:02:15.866 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 18561773 reads 0:02:20.411 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 22283309 reads 0:02:24.897 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 26083238 reads 0:02:29.214 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 29652318 reads 0:02:33.497 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 33208927 reads 0:02:37.992 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 36909027 reads 0:02:42.600 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 40832952 reads 0:03:15.219 4641M / 4975M INFO General (kmer_splitters.hpp : 125) Processed 67605139 reads 0:04:35.843 1M / 5405M INFO General (kmer_splitters.hpp : 131) Used 132406408 reads 0:04:35.854 1M / 5405M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:05:03.962 1M / 5405M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 2244618577 kmers in total. 0:05:03.962 1M / 5405M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:05:03.978 1M / 5405M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:05:03.978 1M / 5405M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:05:03.978 1M / 5405M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:05:03.978 1M / 5405M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:05:03.978 1M / 5405M INFO General (kmer_splitter.hpp : 101) Using cell size of 419430 0:05:04.606 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 5377873 kmers 0:05:05.124 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 12495899 kmers 0:05:05.816 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 21423532 kmers 0:05:06.421 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 29027528 kmers 0:05:07.174 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 38642385 kmers 0:05:07.970 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 48333743 kmers 0:05:08.722 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 57555055 kmers 0:05:09.409 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 66017503 kmers 0:05:10.204 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 75882647 kmers 0:05:11.066 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 86850282 kmers 0:05:12.018 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 98487826 kmers 0:05:12.948 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 109792215 kmers 0:05:13.855 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 120247894 kmers 0:05:14.756 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 131417766 kmers 0:05:15.687 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 142840317 kmers 0:05:16.538 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 153541380 kmers 0:05:17.452 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 163965566 kmers 0:05:18.139 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 172624956 kmers 0:05:26.278 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 272522796 kmers 0:05:48.047 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 547001745 kmers 0:06:29.932 4641M / 5405M INFO General (kmer_splitters.hpp : 194) Processed 1079169298 kmers 0:07:55.210 4641M / 5938M INFO General (kmer_splitters.hpp : 194) Processed 2151120184 kmers 0:08:02.720 4641M / 5938M INFO General (kmer_splitters.hpp : 199) Used 2244628697 kmers. 0:08:02.721 1M / 5938M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:08:51.506 1M / 11G INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 2253443189 kmers in total. 0:08:51.506 1M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:09:28.516 1617M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 2253443189 kmers, 1627639608 bytes occupied (5.77832 bits per kmer). 0:09:28.516 1617M / 11G INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:10:31.651 3769M / 11G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:15:28.629 3769M / 11G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:15:28.804 3769M / 11G INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 0:15:28.805 3769M / 11G INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 0:16:46.771 3927M / 11G INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 1378992 0:16:46.771 3769M / 11G INFO Early A/T remover (early_simplification.hpp : 179) 1350669 50-mers were removed by early poly A/T remover 0:16:46.870 3769M / 11G INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 0:22:34.178 3849M / 11G INFO Early A/T remover (early_simplification.hpp : 330) Clipped tips: 788939 0:22:34.178 3769M / 11G INFO Early A/T remover (early_simplification.hpp : 265) 10652430 50-mers were removed by early poly A/T tip clipper 0:22:34.422 3769M / 11G INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 0:22:34.422 3769M / 11G INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 0:22:34.422 3769M / 11G INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 0:25:17.517 4409M / 11G INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 7018217 0:25:18.485 4409M / 11G INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 7170635 0:25:18.598 3769M / 11G INFO Early tip clipping (early_simplification.hpp : 49) 232795784 50-mers were removed by early tip clipper 0:25:18.599 3769M / 11G INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:25:18.602 3769M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:31:53.025 5542M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 31135238 sequences extracted 0:34:18.843 5542M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:35:16.549 5607M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 11353 loops collected 0:35:17.322 5542M / 11G INFO General (debruijn_graph_constructor: 487) Total 62293182 edges to create 0:35:17.323 7942M / 11G INFO General (debruijn_graph_constructor: 489) Collecting link records 0:35:33.488 8894M / 11G INFO General (debruijn_graph_constructor: 491) Ordering link records 0:35:34.298 8894M / 11G INFO General (debruijn_graph_constructor: 493) Sorting done 0:35:34.550 9407M / 11G INFO General (debruijn_graph_constructor: 503) Total 40440613 vertices to create 0:35:34.551 13G / 13G INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:36:05.674 11G / 14G INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:36:05.674 11G / 14G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:36:40.971 13G / 15G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 2244618577 kmers, 1621266064 bytes occupied (5.77832 bits per kmer). 0:36:42.215 21G / 23G INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:41:35.991 21G / 23G INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:42:09.259 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 8000000 edges 0:42:42.361 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 16000000 edges 0:43:14.869 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 24000000 edges 0:43:47.927 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 32000000 edges 0:44:21.756 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 40000000 edges 0:44:55.405 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 48000000 edges 0:45:28.411 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 56000000 edges 0:45:54.572 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 62292835 edges 0:46:13.584 7582M / 23G INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:46:21.384 7584M / 23G INFO ThresholdFinder (ec_threshold_finder.hpp : 117) Bucket size: 5 0:46:21.387 7584M / 23G INFO General (genomic_info_filler.cpp : 39) Average edge coverage: 3.16015 0:46:21.387 7584M / 23G INFO General (genomic_info_filler.cpp : 40) Graph threshold: 180 0:46:21.395 7582M / 23G INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 3.16015 0:46:21.395 7582M / 23G INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:46:21.395 7582M / 23G INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:46:21.395 7582M / 23G INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 0:46:21.395 7582M / 23G INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 0:46:22.557 7582M / 23G INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 0:46:22.557 7582M / 23G INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 0:46:26.532 7576M / 23G INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 235643 times 0:46:26.540 7576M / 23G INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 0:47:12.513 7576M / 23G INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 23/16454/182 0:47:12.514 7576M / 23G INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 6/141/587 0:47:12.514 7571M / 23G INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:47:12.514 7571M / 23G INFO General (simplification.cpp : 368) Graph simplification started 0:47:12.514 7571M / 23G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:47:12.514 7571M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:47:12.514 7571M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:47:12.514 7571M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:47:17.046 7558M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 477936 times 0:47:17.073 7558M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:47:22.217 7538M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 1303958 times 0:47:22.273 7538M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:48:45.834 7594M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 1119893 times 0:48:45.886 7594M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:48:47.180 7526M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 7258 times 0:48:47.182 7526M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:48:48.156 7490M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 7866 times 0:48:48.158 7490M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:48:48.221 7450M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 481 times 0:48:48.221 7450M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:48:48.225 7449M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 11 times 0:48:48.225 7449M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:48:48.226 7449M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 1 times 0:48:48.226 7449M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:48:48.226 7449M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:48:48.226 7449M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:48:48.226 7449M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:48:48.226 7449M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:48:48.226 7449M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:48:48.226 7449M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:48:48.226 7449M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:48:48.226 7449M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:48:51.261 7714M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:49:26.552 7526M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 3702198 times 0:49:26.751 7526M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:49:26.751 7526M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:28.310 7437M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 62546 times 0:49:28.322 7437M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:30.042 7365M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 93921 times 0:49:30.065 7365M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:36.108 7239M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 18330 times 0:49:36.116 7239M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:36.205 7235M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 471 times 0:49:36.206 7235M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:36.251 7232M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:49:36.251 7232M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:36.257 7226M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 2 times 0:49:36.258 7226M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:36.258 7226M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:49:36.258 7226M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:36.258 7226M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:49:36.258 7226M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:36.258 7226M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:49:36.258 7226M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:49:37.116 7092M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:49:37.537 7098M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 54543 times 0:49:37.556 7098M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:49:37.556 7098M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:38.755 7095M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 6287 times 0:49:38.756 7095M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:39.910 7093M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 1255 times 0:49:39.910 7093M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:42.418 7078M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 1518 times 0:49:42.418 7078M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:42.426 7077M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:49:42.426 7077M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:42.431 7076M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:49:42.431 7076M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:42.431 7076M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:49:42.431 7076M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:49:43.234 7075M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:49:43.330 7077M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 14004 times 0:49:43.334 7077M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:49:43.334 7077M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:44.440 7076M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1556 times 0:49:44.440 7076M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:45.546 7075M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 101 times 0:49:45.546 7075M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:47.437 7073M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 528 times 0:49:47.438 7073M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:47.440 7073M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:49:47.440 7073M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:47.442 7072M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:49:47.442 7072M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:47.442 7072M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:49:47.442 7072M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:49:48.255 7071M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:49:48.299 7072M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 6524 times 0:49:48.299 7072M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:49:48.299 7072M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:49.405 7072M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 637 times 0:49:49.405 7072M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:50.520 7072M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 12 times 0:49:50.521 7072M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:52.191 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 294 times 0:49:52.192 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:52.193 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:49:52.193 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:52.194 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:49:52.194 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:52.194 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:49:52.194 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:49:52.987 7070M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:49:53.013 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 3714 times 0:49:53.013 7070M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:49:53.013 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:54.118 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 355 times 0:49:54.119 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:55.229 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:49:55.230 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:56.805 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 182 times 0:49:56.805 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:56.806 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:49:56.806 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:56.807 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:49:56.807 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:49:56.807 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:49:56.807 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:49:57.598 7069M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:49:57.614 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 2436 times 0:49:57.614 7070M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:49:57.614 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:49:58.715 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 251 times 0:49:58.715 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:49:59.830 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:49:59.831 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:01.344 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 110 times 0:50:01.344 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:01.345 7070M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:50:01.345 7070M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:01.346 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:01.346 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:01.346 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:50:01.346 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:50:02.131 7069M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:50:02.142 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1641 times 0:50:02.142 7069M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:50:02.143 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:03.242 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 165 times 0:50:03.243 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:04.353 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:04.354 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:05.848 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 91 times 0:50:05.849 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:05.849 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:50:05.850 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:05.850 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:05.850 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:05.850 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:50:05.850 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:50:06.641 7069M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:50:06.649 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1216 times 0:50:06.650 7069M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:50:06.650 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:07.746 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 134 times 0:50:07.746 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:08.879 7069M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:08.880 7069M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:10.323 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 50 times 0:50:10.323 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:10.324 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:50:10.324 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:10.324 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:10.324 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:10.324 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:50:10.324 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:50:11.114 7071M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:50:11.121 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 900 times 0:50:11.121 7071M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:50:11.121 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:12.220 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 100 times 0:50:12.221 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:13.327 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:13.328 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:14.762 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 43 times 0:50:14.762 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:14.762 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:50:14.763 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:14.763 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:14.763 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:14.763 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:50:14.763 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:50:15.555 7071M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:50:15.561 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 727 times 0:50:15.561 7071M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:50:15.561 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:16.661 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 72 times 0:50:16.661 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:17.773 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:17.773 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:19.192 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 32 times 0:50:19.193 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:19.193 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:50:19.193 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:19.193 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:19.193 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:19.193 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:50:19.193 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:50:19.980 7071M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:50:19.981 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 5 times 0:50:19.981 7071M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 12 0:50:19.981 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:19.981 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 0:50:19.981 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:19.981 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:19.981 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:50:19.982 7071M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:50:19.982 7071M / 23G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 13 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:50:19.982 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:50:19.983 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:50:19.983 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:50:19.983 7071M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:50:19.983 7071M / 23G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:50:19.983 7071M / 23G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:50:20.633 7068M / 23G INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 0:50:20.633 7068M / 23G INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 0:50:20.633 7068M / 23G INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 0:50:20.633 7068M / 23G INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 0:50:20.633 7068M / 23G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:50:20.633 7068M / 23G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:50:20.633 7068M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:50:22.340 7068M / 23G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 4230 times 0:50:22.341 7068M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:50:23.714 7066M / 23G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 52099 times 0:50:23.726 7066M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:51:23.408 7065M / 23G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 6144 times 0:51:23.409 7065M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:24.495 7065M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 551 times 0:51:24.495 7065M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:51:26.767 7065M / 23G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 219257 times 0:51:26.803 7065M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:28.469 7063M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 2292 times 0:51:28.471 7063M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:51:29.521 7064M / 23G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 7 times 0:51:29.522 7064M / 23G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:51:31.996 7064M / 23G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 5548 times 0:51:31.996 7064M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:51:33.772 7060M / 23G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 10490 times 0:51:33.775 7060M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:51:34.715 7060M / 23G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 565 times 0:51:34.715 7060M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:52:34.765 7060M / 23G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 396 times 0:52:34.765 7060M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:35.850 7056M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 53 times 0:52:35.851 7056M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:52:36.918 7055M / 23G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 2464 times 0:52:36.919 7055M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:37.907 7051M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 367 times 0:52:37.907 7051M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:52:38.858 7051M / 23G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:52:38.859 7051M / 23G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:52:41.332 7050M / 23G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 501 times 0:52:41.333 7050M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:52:41.339 7050M / 23G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 274 times 0:52:41.339 7050M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:52:42.263 7050M / 23G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 92 times 0:52:42.264 7050M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:53:35.666 7050M / 23G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 5 times 0:53:35.667 7050M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:53:35.670 7050M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:53:35.670 7050M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:53:35.671 7050M / 23G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 64 times 0:53:35.672 7050M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:53:35.684 7050M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 6 times 0:53:35.684 7050M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:53:35.693 7050M / 23G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:53:35.693 7050M / 23G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:53:35.693 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 1 times 0:53:35.693 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:53:35.693 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 23 times 0:53:35.693 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:53:36.629 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 2 times 0:53:36.629 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:54:33.433 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 0:54:33.433 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:54:33.433 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:54:33.434 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:54:33.434 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 2 times 0:54:33.434 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:54:33.435 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:54:33.435 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:54:33.435 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:54:33.435 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:54:33.435 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:54:33.435 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:54:33.435 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 0:54:33.435 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:54:34.357 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 0:54:34.358 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:55:34.401 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 0:55:34.401 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:55:34.401 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:55:34.402 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:55:34.402 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 0:55:34.402 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:55:34.402 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:55:34.402 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:55:34.402 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:55:34.402 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:55:34.402 7049M / 23G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:55:34.402 7049M / 23G INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 0:55:44.055 7049M / 23G INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 0:56:00.885 6647M / 23G INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 11331637 times 0:56:01.034 6517M / 23G INFO General (simplification.cpp : 491) Counting average coverage 0:56:02.224 6517M / 23G INFO General (simplification.cpp : 497) Average coverage = 7.26142 0:56:02.224 6517M / 23G INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:56:02.225 6517M / 23G INFO General (read_converter.cpp : 102) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K49/simplified_contigs 0:56:02.230 6520M / 23G INFO General (binary_converter.cpp : 96) 16384 reads processed 0:56:02.234 6520M / 23G INFO General (binary_converter.cpp : 96) 32768 reads processed 0:56:02.240 6520M / 23G INFO General (binary_converter.cpp : 96) 65536 reads processed 0:56:02.267 6520M / 23G INFO General (binary_converter.cpp : 96) 131072 reads processed 0:56:02.345 6520M / 23G INFO General (binary_converter.cpp : 96) 262144 reads processed 0:56:02.465 6520M / 23G INFO General (binary_converter.cpp : 96) 524288 reads processed 0:56:02.689 6520M / 23G INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:56:03.157 6520M / 23G INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:56:03.712 6520M / 23G INFO General (binary_converter.cpp : 111) 3277943 reads written 0:56:03.716 6517M / 23G INFO General (pipeline.cpp : 287) SPAdes finished 0:56:06.008 1M / 23G INFO General (main.cpp : 136) Assembling time: 0 hours 56 minutes 6 seconds ===== K49 finished. ===== K73 started. == Running: /SPAdes-3.15.2-Linux/bin/spades-core /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/configs/config.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/configs/mda_mode.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/configs/rna_mode.info 0:00:00.000 1M / 18M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/configs/config.info 0:00:00.000 1M / 18M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/configs/mda_mode.info 0:00:00.000 1M / 18M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/configs/rna_mode.info 0:00:00.000 1M / 18M INFO General (memory_limit.cpp : 48) Memory limit set to 120 Gb 0:00:00.000 1M / 18M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.2, git revision aab988a9b4986906b38396da7233bb1ee02982f2 0:00:00.000 1M / 18M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.000 1M / 18M INFO General (main.cpp : 109) Assembling dataset (/pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/dataset.info) with K=73 0:00:00.000 1M / 18M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 8 0:00:00.000 1M / 18M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.000 1M / 18M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.000 1M / 18M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.000 1M / 18M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.000 1M / 18M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.000 1M / 18M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:00.000 1M / 18M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 0:00:00.000 1M / 18M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.001 1M / 18M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.002 1M / 18M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:00:00.002 1M / 18M INFO General (construction.cpp : 118) Contigs from previous K will be used: /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K49/simplified_contigs 0:00:00.008 1M / 18M INFO General (construction.cpp : 153) Max read length 150 0:00:00.008 1M / 18M INFO General (construction.cpp : 159) Average read length 149.255 0:00:00.008 1M / 18M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:00:00.008 1M / 18M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:00:00.008 1M / 18M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:00:00.008 1M / 18M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:00:00.008 1M / 18M INFO General (kmer_splitter.hpp : 101) Using cell size of 279620 0:00:03.679 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 3268605 reads 0:00:07.416 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 6641062 reads 0:00:11.098 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 9994668 reads 0:00:14.661 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 13317113 reads 0:00:18.219 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 16546173 reads 0:00:21.750 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 19812329 reads 0:00:25.384 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 23110260 reads 0:00:29.197 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 26504765 reads 0:00:32.800 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 29989571 reads 0:00:36.383 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 33151526 reads 0:00:39.964 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 36510327 reads 0:01:14.091 4641M / 5247M INFO General (kmer_splitters.hpp : 125) Processed 67678597 reads 0:02:41.170 4641M / 5631M INFO General (kmer_splitters.hpp : 125) Processed 134228458 reads 0:02:58.507 1M / 5631M INFO General (kmer_splitters.hpp : 131) Used 138962294 reads 0:02:58.517 1M / 5631M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:03:38.740 1M / 6676M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 1950995460 kmers in total. 0:03:38.740 1M / 6676M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:03:38.755 1M / 6676M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:03:38.755 1M / 6676M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:03:38.756 1M / 6676M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:03:38.756 1M / 6676M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:03:38.756 1M / 6676M INFO General (kmer_splitter.hpp : 101) Using cell size of 279620 0:03:39.375 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 3530502 kmers 0:03:39.908 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 8403949 kmers 0:03:40.453 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 13441076 kmers 0:03:41.070 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 19453970 kmers 0:03:41.638 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 24316093 kmers 0:03:42.301 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 30459025 kmers 0:03:42.989 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 36705246 kmers 0:03:43.729 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 43360804 kmers 0:03:44.402 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 49178083 kmers 0:03:45.060 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 54879897 kmers 0:03:45.611 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 59925318 kmers 0:03:46.390 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 66904889 kmers 0:03:47.155 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 73398820 kmers 0:03:47.962 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 80780519 kmers 0:03:48.802 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 88316731 kmers 0:03:49.613 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 95879564 kmers 0:03:50.411 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 102561952 kmers 0:03:54.299 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 137777706 kmers 0:04:08.992 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 268441135 kmers 0:04:38.907 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 539604009 kmers 0:05:39.783 4641M / 6676M INFO General (kmer_splitters.hpp : 194) Processed 1078035568 kmers 0:07:21.057 4641M / 6676M INFO General (kmer_splitters.hpp : 199) Used 1951009540 kmers. 0:07:21.058 1M / 6676M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:08:17.323 1M / 11G INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 1965932135 kmers in total. 0:08:17.323 1M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:09:13.079 1405M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1965932135 kmers, 1419979792 bytes occupied (5.77835 bits per kmer). 0:09:13.079 1405M / 11G INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:10:46.196 3281M / 11G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:15:21.902 3281M / 11G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:15:21.906 3281M / 11G INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 0:15:21.906 3281M / 11G INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 0:16:49.136 3335M / 11G INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 615154 0:16:49.137 3281M / 11G INFO Early A/T remover (early_simplification.hpp : 179) 611889 74-mers were removed by early poly A/T remover 0:16:49.254 3281M / 11G INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 0:22:21.065 3361M / 11G INFO Early A/T remover (early_simplification.hpp : 330) Clipped tips: 846230 0:22:21.065 3281M / 11G INFO Early A/T remover (early_simplification.hpp : 265) 20357761 74-mers were removed by early poly A/T tip clipper 0:22:21.333 3281M / 11G INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:22:21.336 3281M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:28:57.322 5402M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 36651629 sequences extracted 0:31:14.902 5402M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:31:58.475 5406M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 668 loops collected 0:31:59.332 5402M / 11G INFO General (debruijn_graph_constructor: 487) Total 73304594 edges to create 0:31:59.365 8223M / 11G INFO General (debruijn_graph_constructor: 489) Collecting link records 0:32:18.148 9344M / 11G INFO General (debruijn_graph_constructor: 491) Ordering link records 0:32:19.140 9344M / 12G INFO General (debruijn_graph_constructor: 493) Sorting done 0:32:19.414 10G / 12G INFO General (debruijn_graph_constructor: 503) Total 51613666 vertices to create 0:32:19.416 15G / 15G INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:32:59.524 13G / 16G INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:32:59.524 13G / 16G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:33:48.789 14G / 16G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1950995460 kmers, 1409192832 bytes occupied (5.77835 bits per kmer). 0:33:49.901 21G / 23G INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:37:59.012 21G / 23G INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:38:26.030 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 8000000 edges 0:38:53.073 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 16000000 edges 0:39:20.119 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 24000000 edges 0:39:47.605 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 32000000 edges 0:40:15.020 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 40000000 edges 0:40:41.626 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 48000000 edges 0:41:08.228 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 56000000 edges 0:41:34.764 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 64000000 edges 0:42:02.288 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 72000000 edges 0:42:06.931 21G / 23G INFO General (coverage_filling.hpp : 82) Processed 73304524 edges 0:42:21.118 9222M / 23G INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:42:29.326 9224M / 23G INFO ThresholdFinder (ec_threshold_finder.hpp : 117) Bucket size: 5 0:42:29.332 9224M / 23G INFO General (genomic_info_filler.cpp : 39) Average edge coverage: 2.59406 0:42:29.332 9224M / 23G INFO General (genomic_info_filler.cpp : 40) Graph threshold: 126 0:42:29.338 9222M / 23G INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 2.59406 0:42:29.338 9222M / 23G INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:42:29.338 9222M / 23G INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 0:42:29.348 9231M / 23G INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:42:45.180 11G / 23G INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 45965826 out of 73304524, length: 18446744072693530898 0:42:48.918 11G / 23G INFO General (edge_index.hpp : 167) Using small index (max_id = 73671119) 0:43:00.372 11G / 23G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:48:22.921 12G / 23G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1817420607 kmers, 1312658840 bytes occupied (5.77812 bits per kmer). 0:48:24.552 26G / 29G INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:50:30.171 26G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:50:30.315 26G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:50:31.074 26G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:50:31.579 26G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:50:31.882 26G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:50:32.397 26G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:50:33.519 26G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:50:37.331 26G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:50:44.051 26G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 0:50:57.268 26G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 16937602 reads 0:52:01.836 27G / 29G INFO General (sequence_mapper_notifier.h: 95) Total 33101602 reads processed 0:52:19.507 12G / 29G INFO General (gap_closer.cpp : 452) Initializing gap closer 0:52:20.023 12G / 29G INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:53:41.002 15G / 29G INFO GapCloser (gap_closer.cpp : 393) Closing short gaps complete: filled 348281 gaps after checking 3056680 candidates 0:53:43.957 15G / 29G INFO General (gap_closer.cpp : 456) Gap closer done 0:53:48.616 12G / 29G INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:53:48.617 12G / 29G INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 0:53:48.617 12G / 29G INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 0:53:49.994 12G / 29G INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 0:53:49.994 12G / 29G INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 0:53:56.822 12G / 29G INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 669760 times 0:53:56.857 12G / 29G INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 0:54:51.567 12G / 29G INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 32/3408/143 0:54:51.567 12G / 29G INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 1/28/49 0:54:51.567 12G / 29G INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:54:51.567 12G / 29G INFO General (simplification.cpp : 368) Graph simplification started 0:54:51.567 12G / 29G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:54:51.568 12G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:54:51.568 12G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:54:51.568 12G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:55:25.761 12G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 6079911 times 0:55:26.189 12G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:55:33.366 12G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 1400637 times 0:55:33.414 12G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:56:29.458 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 200488 times 0:56:29.487 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:56:30.119 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2809 times 0:56:30.127 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:56:30.346 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 781 times 0:56:30.353 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:56:30.389 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 61 times 0:56:30.396 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:56:30.403 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:56:30.409 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:56:30.415 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:56:30.421 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:56:30.427 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:56:30.433 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:56:32.168 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:56:42.873 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1330763 times 0:56:42.939 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:56:42.946 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:56:44.714 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 69557 times 0:56:44.733 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:56:46.463 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 50994 times 0:56:46.480 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:56:50.371 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 5732 times 0:56:50.381 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:56:50.430 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 266 times 0:56:50.439 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:56:50.457 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:56:50.466 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:56:50.477 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 3 times 0:56:50.483 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:56:50.490 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:56:50.496 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:56:50.502 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:56:50.508 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:56:50.515 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:56:50.521 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:56:51.502 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:56:51.680 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 24363 times 0:56:51.689 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:56:51.697 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:56:53.076 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 8026 times 0:56:53.084 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:56:54.505 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 81 times 0:56:54.512 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:56:55.948 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 429 times 0:56:55.958 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:56:55.968 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:56:55.976 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:56:55.985 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:56:55.992 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:56:55.999 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:56:56.007 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:56:56.911 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:56:56.958 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 5915 times 0:56:56.965 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:56:56.972 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:56:58.396 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2304 times 0:56:58.404 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:56:59.714 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 4 times 0:56:59.722 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:00.912 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 169 times 0:57:00.921 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:00.929 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:57:00.936 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:00.944 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:00.950 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:00.956 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:57:00.962 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:57:01.832 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:57:01.857 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 2563 times 0:57:01.864 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:57:01.871 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:03.274 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1011 times 0:57:03.281 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:04.592 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:04.600 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:05.779 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 71 times 0:57:05.788 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:05.796 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:57:05.803 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:05.811 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:05.818 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:05.825 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:57:05.831 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:57:06.792 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:57:06.811 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1496 times 0:57:06.819 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:57:06.826 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:08.249 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 576 times 0:57:08.257 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:09.675 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:09.684 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:10.841 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 39 times 0:57:10.850 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:10.858 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:57:10.865 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:10.873 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:10.880 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:10.887 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:57:10.893 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:57:11.773 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:57:11.787 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 894 times 0:57:11.794 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:57:11.801 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:13.207 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 320 times 0:57:13.215 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:14.541 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:14.550 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:15.684 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 24 times 0:57:15.693 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:15.701 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:57:15.708 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:15.715 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:15.722 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:15.728 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:57:15.735 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:57:16.704 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:57:16.716 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 613 times 0:57:16.723 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:57:16.729 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:18.126 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 206 times 0:57:18.135 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:19.467 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:19.476 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:20.628 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 10 times 0:57:20.636 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:20.644 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:57:20.651 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:20.659 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:20.667 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:20.675 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:57:20.682 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:57:21.635 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:57:21.647 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 427 times 0:57:21.654 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:57:21.662 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:22.988 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 131 times 0:57:22.997 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:24.315 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:24.324 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:25.382 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 8 times 0:57:25.391 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:25.399 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:57:25.406 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:25.414 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:25.422 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:25.430 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:57:25.438 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:57:26.398 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:57:26.409 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 331 times 0:57:26.417 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:57:26.424 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:27.747 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 92 times 0:57:27.756 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:29.077 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:29.086 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:30.219 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 7 times 0:57:30.229 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:30.236 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:57:30.244 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:30.252 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:30.260 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:30.267 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:57:30.275 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:57:31.228 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:57:31.237 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 258 times 0:57:31.244 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:57:31.250 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:32.580 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 80 times 0:57:32.588 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:34.013 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:34.021 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:35.132 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 5 times 0:57:35.142 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:35.149 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:57:35.157 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:35.165 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:35.173 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:35.180 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:57:35.187 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:57:36.137 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:57:36.145 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1 times 0:57:36.151 14G / 29G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 12 0:57:36.158 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:57:36.164 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:57:36.171 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:57:36.177 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:57:36.184 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:57:36.190 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:57:36.197 14G / 29G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:57:36.203 14G / 29G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:57:36.210 14G / 29G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:57:36.975 14G / 29G INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 0:57:36.993 14G / 29G INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:57:44.539 15G / 29G INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 33174296 out of 34078668, length: 18446744072626833170 0:57:47.857 15G / 29G INFO General (edge_index.hpp : 167) Using small index (max_id = 147342235) 0:57:56.797 15G / 29G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 1:02:41.305 16G / 29G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1623108960 kmers, 1173706194 bytes occupied (5.78498 bits per kmer). 1:02:42.767 28G / 29G INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 1:04:33.291 28G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 1:04:33.316 28G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 1:04:34.573 28G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 1:04:36.439 28G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 1:04:36.789 29G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 1:04:36.885 29G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 1:04:40.371 29G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 1:04:47.709 29G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 1:05:02.449 29G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 1:05:31.129 29G / 29G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 1:07:46.086 30G / 30G INFO General (sequence_mapper_notifier.h: 95) Total 33101602 reads processed 1:08:03.085 16G / 30G INFO General (gap_closer.cpp : 452) Initializing gap closer 1:08:03.660 16G / 30G INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 1:08:39.481 16G / 30G INFO GapCloser (gap_closer.cpp : 393) Closing short gaps complete: filled 48064 gaps after checking 2172936 candidates 1:08:40.558 16G / 30G INFO General (gap_closer.cpp : 456) Gap closer done 1:08:43.711 14G / 30G INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 1:08:43.816 14G / 30G INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 1:08:43.827 14G / 30G INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 1:08:43.834 14G / 30G INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 1:08:43.840 14G / 30G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:08:43.849 14G / 30G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:08:43.859 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 1:08:46.135 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 1302 times 1:08:46.143 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 1:08:47.804 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 79099 times 1:08:47.818 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 1:10:08.589 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 1606 times 1:10:08.597 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 1:10:09.876 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 903 times 1:10:09.884 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 1:10:12.594 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 273854 times 1:10:12.619 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 1:10:14.723 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 2233 times 1:10:14.731 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 1:10:15.855 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 1:10:15.863 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 1:10:18.908 14G / 30G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 10855 times 1:10:18.916 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 1:10:21.267 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 3195 times 1:10:21.278 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 1:10:22.815 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 176 times 1:10:22.823 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 1:11:29.822 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 263 times 1:11:29.830 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 1:11:31.003 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 40 times 1:11:31.012 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 1:11:32.190 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 1349 times 1:11:32.199 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 1:11:33.143 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 188 times 1:11:33.152 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 1:11:34.026 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 1:11:34.034 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 1:11:36.616 14G / 30G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 43 times 1:11:36.624 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 1:11:36.632 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 53 times 1:11:36.639 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 1:11:37.567 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 3 times 1:11:37.576 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 1:12:37.420 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 7 times 1:12:37.427 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 1:12:37.436 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 1:12:37.443 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 1:12:37.449 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 18 times 1:12:37.456 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 1:12:37.464 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 4 times 1:12:37.471 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 1:12:37.478 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 1:12:37.484 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 1:12:37.491 14G / 30G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 1:12:37.497 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 1:12:37.504 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 3 times 1:12:37.510 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 1:12:38.450 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 1:12:38.459 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 1:13:36.994 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 1:13:37.003 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 1:13:37.011 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 1:13:37.017 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 1:13:37.024 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 2 times 1:13:37.030 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 1:13:37.037 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 1:13:37.043 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 1:13:37.050 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 1:13:37.056 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 1:13:37.062 14G / 30G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 1:13:37.069 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 1:13:37.075 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 1:13:37.082 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 1:13:38.048 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 1:13:38.056 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 1:14:37.234 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 1:14:37.243 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 1:14:37.251 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 1:14:37.257 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 1:14:37.264 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 1:14:37.270 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 1:14:37.277 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 1:14:37.283 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 1:14:37.290 14G / 30G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 1:14:37.296 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 1:14:37.302 14G / 30G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 1:14:37.309 14G / 30G INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 1:14:47.578 14G / 30G INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 1:15:07.325 13G / 30G INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 13737807 times 1:15:07.528 13G / 30G INFO General (simplification.cpp : 491) Counting average coverage 1:15:08.367 13G / 30G INFO General (simplification.cpp : 497) Average coverage = 6.27363 1:15:08.375 13G / 30G INFO StageManager (stage.cpp : 185) STAGE == Mismatch Correction (id: mismatch_correction) 1:15:08.382 13G / 30G INFO General (graph_pack.cpp : 67) Index refill 1:15:08.389 13G / 30G INFO General (edge_index.hpp : 156) Using small index (max_id = 147342235) 1:15:10.780 13G / 30G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 1:16:18.722 14G / 30G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 500882538 kmers, 362316070 bytes occupied (5.78684 bits per kmer). 1:16:19.180 17G / 30G INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 1:16:51.340 17G / 30G INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 35011780 kmers to process 1:17:00.741 17G / 30G INFO General (graph_pack.cpp : 79) Normalizing done 1:17:00.749 17G / 30G INFO General (mismatch_correction.cpp : 400) Collect potential mismatches 1:17:10.047 17G / 30G INFO General (mismatch_correction.cpp : 193) Total 195116 edges (out of 5129624) with 2526666 potential mismatch positions (12.9496 positions per edge) 1:17:10.077 17G / 30G INFO General (mismatch_correction.cpp : 402) Potential mismatches collected 1:17:12.009 17G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 1:17:12.416 17G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 1:17:13.785 17G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 1:17:14.350 17G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 1:17:15.377 17G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 1:17:15.548 17G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 1:17:18.599 17G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 1:17:25.535 17G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 1:17:35.327 17G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 1:17:56.642 17G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 1:18:42.853 18G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 1:20:15.239 18G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 67150800 reads 1:29:21.137 18G / 30G INFO General (sequence_mapper_notifier.h: 95) Total 132406408 reads processed 1:29:28.788 18G / 30G INFO General (mismatch_correction.cpp : 395) All edges processed 1:29:28.889 17G / 30G INFO General (mismatch_correction.cpp : 450) Corrected 4195 nucleotides 1:29:28.936 17G / 30G INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 1:29:28.943 17G / 30G INFO General (contig_output.hpp : 16) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/before_rr.fasta 1:29:41.353 17G / 30G INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/assembly_graph_after_simplification.gfa 1:29:47.618 17G / 30G INFO StageManager (stage.cpp : 185) STAGE == Paired Information Counting (id: late_pair_info_count) 1:29:56.917 18G / 30G INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 35371605 kmers to process 1:30:06.383 18G / 30G INFO General (graph_pack.cpp : 79) Normalizing done 1:30:06.818 18G / 30G INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 500 1:30:06.829 18G / 30G INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 1:30:06.837 18G / 30G INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 1:30:06.863 19G / 30G INFO General (pair_info_count.cpp : 48) Selecting usual mapper 1:30:15.119 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 1:30:16.547 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 1:30:17.559 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 1:30:19.334 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 1:30:23.996 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 1:30:25.077 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 1:30:32.039 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 1:30:46.481 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 1:31:17.508 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 1:32:22.827 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 1:38:52.327 19G / 30G INFO General (sequence_mapper_notifier.h: 95) Total 33101602 reads processed 1:38:52.600 19G / 30G INFO General (pair_info_count.cpp : 220) Edge pairs: 18933966 1:38:52.609 19G / 30G INFO General (pair_info_count.cpp : 224) 2979051 paired reads (8.99972% of all) aligned to long edges 1:38:52.618 18G / 30G INFO General (pair_info_count.cpp : 373) Insert size = 314.536, deviation = 117.221, left quantile = 183, right quantile = 476, read length = 150 1:38:52.626 18G / 30G INFO General (pair_info_count.cpp : 402) Mapping library #0 1:38:52.635 18G / 30G INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 1:38:52.643 18G / 30G INFO General (pair_info_count.cpp : 302) Left insert size quantile 183, right insert size quantile 476, filtering threshold 0, rounding threshold 0 1:38:52.661 18G / 30G INFO General (pair_info_count.cpp : 48) Selecting usual mapper 1:39:04.906 18G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 1:39:10.755 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 1:39:12.039 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 1:39:16.255 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 1:39:18.542 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 1:39:18.923 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 1:39:40.642 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 1:40:11.200 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 1:41:10.773 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 1:43:26.868 19G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 2:38:40.427 22G / 30G INFO General (sequence_mapper_notifier.h: 95) Total 33101602 reads processed 2:38:41.462 22G / 30G INFO General (pair_info_count.cpp : 411) Mapping single reads of library #0 2:38:41.473 22G / 30G INFO General (pair_info_count.cpp : 266) Will calculate lib coverage as well 2:38:41.484 22G / 30G INFO General (pair_info_count.cpp : 48) Selecting usual mapper 2:38:44.326 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 2:38:44.837 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 2:38:45.732 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 2:38:46.585 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 2:38:47.730 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 2:38:48.967 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 2:38:51.340 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 2:38:57.497 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 2:39:09.582 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 2:39:32.414 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 2:40:19.222 22G / 30G INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 2:44:29.405 22G / 30G INFO General (sequence_mapper_notifier.h: 95) Total 66203204 reads processed 2:44:29.794 22G / 30G INFO General (pair_info_count.cpp : 413) Total paths obtained from single reads: 0 2:44:29.811 22G / 30G INFO StageManager (stage.cpp : 185) STAGE == Distance Estimation (id: distance_estimation) 2:44:29.827 22G / 30G INFO General (distance_estimation.cpp : 179) Processing library #0 2:44:29.845 22G / 30G INFO General (distance_estimation.cpp : 150) Weight Filter Done 2:44:29.862 22G / 30G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 2:46:52.013 23G / 30G INFO General (distance_estimation.cpp : 37) Filtering info 2:46:52.400 23G / 30G INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 99660206 2:47:16.593 22G / 30G INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 15621811 2:47:16.614 22G / 30G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 2:47:19.577 22G / 30G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 2:47:19.594 22G / 30G INFO General (distance_estimation.cpp : 160) Improving paired information 2:48:05.661 22G / 30G INFO PairInfoImprover (pair_info_improver.hpp : 105) Paired info stats: missing = 3832693; contradictional = 0 2:49:27.555 22G / 30G INFO PairInfoImprover (pair_info_improver.hpp : 105) Paired info stats: missing = 818562; contradictional = 0 2:49:27.731 22G / 30G INFO StageManager (stage.cpp : 185) STAGE == Repeat Resolving (id: repeat_resolving) 2:49:27.747 22G / 30G INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 2:49:27.764 22G / 30G INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 2:49:40.318 32G / 32G INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 2:49:40.342 32G / 32G INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 24924069 2:49:40.374 33G / 33G INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 24924069 2:49:41.006 34G / 34G INFO General (extenders_logic.cpp : 543) Using 1 paired-end library 2:49:41.030 34G / 34G INFO General (extenders_logic.cpp : 544) Using 1 paired-end scaffolding library 2:49:41.052 34G / 34G INFO General (extenders_logic.cpp : 545) Using 0 single read libraries 2:49:41.074 34G / 34G INFO General (launcher.cpp : 447) Total number of extenders is 5 2:49:41.096 34G / 34G INFO General (path_extenders.cpp : 36) Processed 0 paths from 2559834 (0%) 2:49:41.166 34G / 34G INFO General (path_extenders.cpp : 34) Processed 128 paths from 2559834 (0%) 2:49:41.202 34G / 34G INFO General (path_extenders.cpp : 34) Processed 256 paths from 2559834 (0%) 2:49:41.259 34G / 34G INFO General (path_extenders.cpp : 34) Processed 512 paths from 2559834 (0%) 2:49:41.328 34G / 34G INFO General (path_extenders.cpp : 34) Processed 1024 paths from 2559834 (0%) 2:49:41.415 34G / 34G INFO General (path_extenders.cpp : 34) Processed 2048 paths from 2559834 (0%) 2:49:41.594 34G / 34G INFO General (path_extenders.cpp : 34) Processed 4096 paths from 2559834 (0%) 2:49:41.980 34G / 34G INFO General (path_extenders.cpp : 34) Processed 8192 paths from 2559834 (0%) 2:49:42.555 34G / 34G INFO General (path_extenders.cpp : 34) Processed 16384 paths from 2559834 (0%) 2:49:43.624 34G / 34G INFO General (path_extenders.cpp : 34) Processed 32768 paths from 2559834 (1%) 2:49:45.444 34G / 34G INFO General (path_extenders.cpp : 34) Processed 65536 paths from 2559834 (2%) 2:49:49.132 35G / 35G INFO General (path_extenders.cpp : 34) Processed 131072 paths from 2559834 (5%) 2:49:55.148 35G / 35G INFO General (path_extenders.cpp : 36) Processed 255984 paths from 2559834 (10%) 2:49:55.399 35G / 35G INFO General (path_extenders.cpp : 34) Processed 262144 paths from 2559834 (10%) 2:50:04.078 36G / 36G INFO General (path_extenders.cpp : 36) Processed 511968 paths from 2559834 (20%) 2:50:04.422 36G / 36G INFO General (path_extenders.cpp : 34) Processed 524288 paths from 2559834 (20%) 2:50:08.989 37G / 37G INFO General (path_extenders.cpp : 36) Processed 767952 paths from 2559834 (30%) 2:50:13.538 38G / 38G INFO General (path_extenders.cpp : 36) Processed 1023936 paths from 2559834 (40%) 2:50:13.794 38G / 38G INFO General (path_extenders.cpp : 34) Processed 1048576 paths from 2559834 (40%) 2:50:16.694 39G / 39G INFO General (path_extenders.cpp : 36) Processed 1279920 paths from 2559834 (50%) 2:50:25.401 40G / 40G INFO General (path_extenders.cpp : 36) Processed 1535904 paths from 2559834 (60%) 2:50:29.410 41G / 41G INFO General (path_extenders.cpp : 36) Processed 1791888 paths from 2559834 (70%) 2:50:46.977 42G / 42G INFO General (path_extenders.cpp : 36) Processed 2047872 paths from 2559834 (80%) 2:50:48.773 42G / 42G INFO General (path_extenders.cpp : 34) Processed 2097152 paths from 2559834 (81%) 2:50:56.599 43G / 43G INFO General (path_extenders.cpp : 36) Processed 2303856 paths from 2559834 (90%) 2:53:41.775 44G / 44G INFO General (launcher.cpp : 250) Finalizing paths 2:53:41.806 44G / 44G INFO General (launcher.cpp : 252) Deduplicating paths 2:53:43.564 44G / 44G INFO General (launcher.cpp : 256) Paths deduplicated 2:53:43.597 44G / 44G INFO General (launcher.cpp : 263) Overlaps will not be removed 2:53:48.941 44G / 44G INFO General (launcher.cpp : 273) Paths finalized 2:53:48.973 44G / 44G INFO General (launcher.cpp : 454) Closing gaps in paths 2:53:56.008 53G / 53G INFO General (launcher.cpp : 484) Gap closing completed 2:53:57.760 54G / 54G INFO General (launcher.cpp : 302) Traversing tandem repeats 2:54:14.398 54G / 54G INFO General (launcher.cpp : 312) Traversed 0 loops 2:54:14.435 54G / 54G INFO General (launcher.cpp : 250) Finalizing paths 2:54:14.471 54G / 54G INFO General (launcher.cpp : 252) Deduplicating paths 2:54:16.300 54G / 54G INFO General (launcher.cpp : 256) Paths deduplicated 2:54:16.336 54G / 54G INFO General (launcher.cpp : 263) Overlaps will not be removed 2:54:20.082 54G / 54G INFO General (launcher.cpp : 273) Paths finalized 2:54:20.116 54G / 54G INFO General (launcher.cpp : 499) Finalizing paths - hard 2:54:22.247 63G / 63G INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 152 2:54:22.286 63G / 63G INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 152 2:54:22.325 63G / 63G INFO General (launcher.cpp : 297) Length cutoff: 152 2:54:22.689 60G / 62G INFO General (launcher.cpp : 295) Read length relative cutoff 2 converted to 227 2:54:22.730 60G / 62G INFO General (launcher.cpp : 296) Read length absolute cutoff 180 bp converted to 227 2:54:22.768 60G / 62G INFO General (launcher.cpp : 297) Length cutoff: 227 2:54:23.721 56G / 62G INFO General (launcher.cpp : 295) Read length relative cutoff 2 converted to 227 2:54:23.761 56G / 62G INFO General (launcher.cpp : 296) Read length absolute cutoff 180 bp converted to 227 2:54:23.801 56G / 62G INFO General (launcher.cpp : 297) Length cutoff: 227 2:54:29.207 54G / 62G INFO General (launcher.cpp : 499) Finalizing paths - soft 2:54:31.512 63G / 63G INFO General (launcher.cpp : 295) Read length relative cutoff 1.05 converted to 84 2:54:31.550 63G / 63G INFO General (launcher.cpp : 296) Read length absolute cutoff 85 bp converted to 84 2:54:31.587 63G / 63G INFO General (launcher.cpp : 297) Length cutoff: 84 2:54:31.804 62G / 62G INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 152 2:54:31.843 62G / 62G INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 152 2:54:31.880 62G / 62G INFO General (launcher.cpp : 297) Length cutoff: 152 2:54:32.082 62G / 62G INFO General (launcher.cpp : 295) Read length relative cutoff 1.2 converted to 107 2:54:32.120 62G / 62G INFO General (launcher.cpp : 296) Read length absolute cutoff 100 bp converted to 107 2:54:32.158 62G / 62G INFO General (launcher.cpp : 297) Length cutoff: 107 2:54:47.410 54G / 62G INFO General (launcher.cpp : 507) Finalizing main paths 2:54:47.458 54G / 62G INFO General (launcher.cpp : 295) Read length relative cutoff 1.3 converted to 122 2:54:47.493 54G / 62G INFO General (launcher.cpp : 296) Read length absolute cutoff 110 bp converted to 122 2:54:47.529 54G / 62G INFO General (launcher.cpp : 297) Length cutoff: 122 2:54:47.923 52G / 62G INFO General (launcher.cpp : 295) Read length relative cutoff 1.6 converted to 167 2:54:47.960 52G / 62G INFO General (launcher.cpp : 296) Read length absolute cutoff 140 bp converted to 167 2:54:47.995 52G / 62G INFO General (launcher.cpp : 297) Length cutoff: 167 2:54:48.573 50G / 62G INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 152 2:54:48.609 50G / 62G INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 152 2:54:48.646 50G / 62G INFO General (launcher.cpp : 297) Length cutoff: 152 2:54:50.545 50G / 62G INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 2:54:57.585 28G / 62G INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 2:54:57.752 28G / 62G INFO General (contig_output.hpp : 16) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/before_rr.fasta 2:55:09.509 28G / 62G INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/assembly_graph_with_scaffolds.gfa 2:55:15.486 28G / 62G INFO General (contig_output_stage.cpp : 165) Outputting FastG graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/assembly_graph.fastg 2:55:42.407 29G / 62G INFO General (contig_output_stage.cpp : 98) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/transcripts.fasta 2:55:44.876 29G / 62G INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/transcripts.paths 2:55:46.766 29G / 62G INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 2:55:48.585 28G / 62G INFO General (pipeline.cpp : 287) SPAdes finished 2:55:59.524 1M / 62G INFO General (main.cpp : 136) Assembling time: 2 hours 55 minutes 59 seconds ===== K73 finished. ===== Copy files started. == Running: /usr/bin/python /SPAdes-3.15.2-Linux/share/spades/spades_pipeline/scripts/copy_files.py /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/before_rr.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/before_rr.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/assembly_graph_after_simplification.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/assembly_graph_after_simplification.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/transcripts.paths /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/transcripts.paths /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/assembly_graph_with_scaffolds.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/assembly_graph_with_scaffolds.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/assembly_graph.fastg /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/assembly_graph.fastg /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/hard_filtered_final_paths.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/hard_filtered_transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/K73/soft_filtered_final_paths.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/soft_filtered_transcripts.fasta ===== Copy files finished. ===== Assembling finished. ===== Breaking scaffolds started. == Running: /usr/bin/python /SPAdes-3.15.2-Linux/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/scaffolds.fasta --misc_dir /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/misc --threshold_for_breaking_scaffolds 3 ===== Breaking scaffolds finished. ===== Terminate started. ===== Terminate finished. * Assembled transcripts are in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/transcripts.fasta * Paths in the assembly graph corresponding to the transcripts are in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/transcripts.paths * Hard filtered transcripts are in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/hard_filtered_transcripts.fasta * Soft filtered transcripts are in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/soft_filtered_transcripts.fasta * Assembly graph is in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/assembly_graph.fastg * Assembly graph in GFA format is in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished. SPAdes log can be found here: /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/3a2c757b-db89-4045-82e6-23ba89439957/call-asse/metatranscriptome_assy/78f51200-8d4d-4fd0-82af-99771790c965/call-assy/execution/out.spades/spades.log Thank you for using SPAdes!