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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades --12 /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/spades.log /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K49/configs/config.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K49/configs/mda_mode.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K49/configs/rna_mode.info 0:00:00.000 1M / 16M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K49/configs/config.info 0:00:00.010 1M / 16M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K49/configs/mda_mode.info 0:00:00.010 1M / 16M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K49/configs/rna_mode.info 0:00:00.010 1M / 16M INFO General (memory_limit.cpp : 48) Memory limit set to 120 Gb 0:00:00.010 1M / 16M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.2, git revision aab988a9b4986906b38396da7233bb1ee02982f2 0:00:00.010 1M / 16M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.010 1M / 16M INFO General (main.cpp : 109) Assembling dataset (/pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/dataset.info) with K=49 0:00:00.010 1M / 16M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 8 0:00:00.010 1M / 16M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.010 1M / 16M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.010 1M / 16M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.010 1M / 16M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.010 1M / 16M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.010 1M / 16M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:00.010 1M / 16M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.012 1M / 16M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.012 1M / 16M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.382 14M / 37M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:00.390 14M / 40M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:00.547 14M / 61M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:00.727 14M / 80M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:01.238 14M / 106M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:02.075 14M / 134M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:00:03.721 14M / 176M INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:00:07.035 14M / 194M INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:00:14.015 14M / 200M INFO General (binary_converter.cpp : 96) 4194304 reads processed 0:00:27.657 14M / 216M INFO General (binary_converter.cpp : 96) 8388608 reads processed 0:00:55.096 14M / 218M INFO General (binary_converter.cpp : 96) 16777216 reads processed 0:01:49.384 14M / 222M INFO General (binary_converter.cpp : 96) 33554432 reads processed 0:02:35.334 14M / 222M INFO General (binary_converter.cpp : 111) 47592957 reads written 0:02:35.334 7M / 222M INFO General (read_converter.cpp : 81) Converting single reads 0:02:35.336 11M / 222M INFO General (binary_converter.cpp : 111) 0 reads written 0:02:35.336 7M / 222M INFO General (read_converter.cpp : 87) Converting merged reads 0:02:35.337 11M / 222M INFO General (binary_converter.cpp : 111) 0 reads written 0:02:35.350 1M / 222M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:02:35.353 1M / 222M INFO General (construction.cpp : 153) Max read length 150 0:02:35.353 1M / 222M INFO General (construction.cpp : 159) Average read length 148.098 0:02:35.353 1M / 222M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:02:35.356 1M / 222M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:02:35.356 1M / 222M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:02:35.356 1M / 222M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:02:35.356 1M / 222M INFO General (kmer_splitter.hpp : 101) Using cell size of 419430 0:02:36.030 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 607730 reads 0:02:36.814 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 1304241 reads 0:02:37.252 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 1729135 reads 0:02:37.678 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 2121688 reads 0:02:38.121 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 2552628 reads 0:02:38.700 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 2945981 reads 0:02:39.408 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 3406361 reads 0:02:40.642 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 4284421 reads 0:02:46.417 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 8588470 reads 0:02:58.998 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 16919044 reads 0:03:23.300 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 33869873 reads 0:04:06.973 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 67221968 reads 0:05:33.620 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 134350494 reads 0:07:39.024 1M / 4056M INFO General (kmer_splitters.hpp : 131) Used 190371828 reads 0:07:39.032 1M / 4056M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:08:16.681 1M / 4133M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 1714383289 kmers in total. 0:08:16.681 1M / 4133M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:08:16.695 1M / 4133M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:08:16.696 1M / 4133M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:08:16.696 1M / 4133M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:08:16.696 1M / 4133M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:08:16.696 1M / 4133M INFO General (kmer_splitter.hpp : 101) Using cell size of 419430 0:08:17.373 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 6834268 kmers 0:08:17.734 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 11261892 kmers 0:08:18.092 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 15554422 kmers 0:08:18.459 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 19676725 kmers 0:08:18.855 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 23848238 kmers 0:08:19.249 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 28177178 kmers 0:08:19.676 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 32776158 kmers 0:08:20.100 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 37180803 kmers 0:08:20.508 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 41506517 kmers 0:08:20.981 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 46609425 kmers 0:08:21.416 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 51191568 kmers 0:08:21.818 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 55311189 kmers 0:08:22.445 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 63097723 kmers 0:08:22.863 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 67138425 kmers 0:08:23.298 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 71684113 kmers 0:08:23.927 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 79340780 kmers 0:08:24.685 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 88383926 kmers 0:08:28.847 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 142214661 kmers 0:08:39.531 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 270047149 kmers 0:09:00.712 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 537966452 kmers 0:09:43.243 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 1074894389 kmers 0:10:34.375 4641M / 4641M INFO General (kmer_splitters.hpp : 199) Used 1714394289 kmers. 0:10:34.376 1M / 4133M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:11:08.935 1M / 6396M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 1710098306 kmers in total. 0:11:08.935 1M / 6396M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:11:37.439 1286M / 6396M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1710098306 kmers, 1235200576 bytes occupied (5.77838 bits per kmer). 0:11:37.439 1286M / 6396M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:12:24.488 2918M / 6396M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:15:56.902 2918M / 6396M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:15:56.947 2918M / 6396M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 0:15:56.947 2918M / 6396M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 0:17:18.307 8698M / 8704M INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 60589380 0:17:18.314 2918M / 8704M INFO Early A/T remover (early_simplification.hpp : 179) 59752119 50-mers were removed by early poly A/T remover 0:17:18.327 2918M / 8704M INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 0:20:45.260 4198M / 8704M INFO Early A/T remover (early_simplification.hpp : 330) Clipped tips: 10292017 0:20:45.261 2918M / 8704M INFO Early A/T remover (early_simplification.hpp : 265) 184734941 50-mers were removed by early poly A/T tip clipper 0:20:45.296 2918M / 8704M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 0:20:45.296 2918M / 8704M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 0:20:45.296 2918M / 8704M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 0:23:15.538 4198M / 8704M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 18804325 0:23:17.900 4198M / 8704M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 19821662 0:23:17.915 2918M / 8704M INFO Early tip clipping (early_simplification.hpp : 49) 441831296 50-mers were removed by early tip clipper 0:23:17.917 2918M / 8704M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:23:17.920 2918M / 8704M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:26:53.795 4266M / 8704M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 26254393 sequences extracted 0:28:05.193 4266M / 8704M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:28:35.840 4274M / 8704M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1822 loops collected 0:28:36.382 4266M / 8704M INFO General (debruijn_graph_constructor: 487) Total 52512430 edges to create 0:28:36.383 6289M / 8704M INFO General (debruijn_graph_constructor: 489) Collecting link records 0:28:45.754 7093M / 8704M INFO General (debruijn_graph_constructor: 491) Ordering link records 0:28:46.397 7093M / 8853M INFO General (debruijn_graph_constructor: 493) Sorting done 0:28:46.627 7605M / 8853M INFO General (debruijn_graph_constructor: 503) Total 41003870 vertices to create 0:28:46.628 12G / 12G INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:29:12.654 9672M / 12G INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:29:12.654 9672M / 12G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:29:40.935 11G / 12G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1714383289 kmers, 1238295248 bytes occupied (5.77838 bits per kmer). 0:29:41.995 18G / 18G INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:32:55.027 18G / 18G INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:33:13.720 18G / 18G INFO General (coverage_filling.hpp : 82) Processed 8000000 edges 0:33:32.852 18G / 18G INFO General (coverage_filling.hpp : 82) Processed 16000000 edges 0:33:52.834 18G / 18G INFO General (coverage_filling.hpp : 82) Processed 24000000 edges 0:34:12.515 18G / 18G INFO General (coverage_filling.hpp : 82) Processed 32000000 edges 0:34:32.167 18G / 18G INFO General (coverage_filling.hpp : 82) Processed 40000000 edges 0:34:51.845 18G / 18G INFO General (coverage_filling.hpp : 82) Processed 48000000 edges 0:35:02.945 18G / 18G INFO General (coverage_filling.hpp : 82) Processed 52512375 edges 0:35:21.042 21G / 46G INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:35:25.420 21G / 46G INFO ThresholdFinder (ec_threshold_finder.hpp : 117) Bucket size: 6 0:35:25.420 21G / 46G INFO General (genomic_info_filler.cpp : 39) Average edge coverage: 5.10717 0:35:25.420 21G / 46G INFO General (genomic_info_filler.cpp : 40) Graph threshold: 124 0:35:25.422 21G / 46G INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 5.10717 0:35:25.422 21G / 46G INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:35:25.422 21G / 46G INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:35:25.422 21G / 46G INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 0:35:25.422 21G / 46G INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 0:35:26.299 21G / 46G INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 0:35:26.299 21G / 46G INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 0:35:43.746 21G / 46G INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 8460235 times 0:35:43.858 21G / 46G INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 0:36:08.529 21G / 46G INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 11/3701/62 0:36:08.530 21G / 46G INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 0/15/36 0:36:08.530 20G / 46G INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:36:08.530 20G / 46G INFO General (simplification.cpp : 368) Graph simplification started 0:36:08.530 20G / 46G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:36:08.530 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:36:08.530 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:36:08.530 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:14.228 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1183378 times 0:36:14.324 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:17.272 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 451055 times 0:36:17.307 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:36.328 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 668319 times 0:36:36.358 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:36.944 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 11427 times 0:36:36.946 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:37.321 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 2389 times 0:36:37.322 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:37.350 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 280 times 0:36:37.350 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:37.351 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 15 times 0:36:37.351 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:37.352 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 1 times 0:36:37.352 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:37.352 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 1 times 0:36:37.352 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:37.352 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:36:37.352 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:37.352 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:37.352 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:37.352 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:36:37.352 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:36:38.104 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:36:39.962 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 258164 times 0:36:39.977 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:36:39.977 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:40.995 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 26925 times 0:36:40.996 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:41.812 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 7760 times 0:36:41.813 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:42.947 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 8427 times 0:36:42.949 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:42.961 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 35 times 0:36:42.961 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:42.968 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:42.968 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:42.968 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 2 times 0:36:42.968 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:42.968 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:36:42.968 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:42.968 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:42.969 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:42.969 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:36:42.969 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:36:43.578 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:36:43.603 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 3480 times 0:36:43.604 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:36:43.604 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:44.486 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2407 times 0:36:44.486 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:45.275 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 86 times 0:36:45.275 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:45.942 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 557 times 0:36:45.942 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:45.943 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 0:36:45.943 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:45.943 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:45.943 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:45.943 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:36:45.943 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:45.943 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:36:45.943 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:45.944 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:45.944 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:45.944 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:36:45.944 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:36:46.538 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:36:46.546 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1024 times 0:36:46.546 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:36:46.546 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:47.372 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 849 times 0:36:47.372 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:48.159 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 2 times 0:36:48.159 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:48.828 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 199 times 0:36:48.828 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:48.829 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:36:48.829 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:48.829 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:48.829 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:48.829 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:36:48.829 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:36:49.421 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:36:49.425 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 549 times 0:36:49.425 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:36:49.425 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:50.261 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 458 times 0:36:50.261 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:51.041 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:51.041 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:51.707 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 90 times 0:36:51.707 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:51.707 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:36:51.707 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:51.707 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:51.707 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:51.707 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:36:51.707 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:36:52.345 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:36:52.348 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 310 times 0:36:52.348 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:36:52.348 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:53.204 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 254 times 0:36:53.204 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:54.024 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:54.025 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:54.684 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 48 times 0:36:54.685 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:54.685 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:36:54.685 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:54.685 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:54.685 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:54.685 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:36:54.685 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:36:55.300 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:36:55.302 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 215 times 0:36:55.303 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:36:55.303 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:56.159 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 166 times 0:36:56.160 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:56.972 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:56.973 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:57.631 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 25 times 0:36:57.631 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:57.631 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:36:57.631 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:57.631 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:57.631 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:36:57.631 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:36:57.631 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:36:58.238 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:36:58.240 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 143 times 0:36:58.240 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:36:58.240 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:36:59.079 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 105 times 0:36:59.079 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:36:59.855 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:36:59.856 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:37:00.492 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 21 times 0:37:00.493 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:37:00.493 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:37:00.493 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:37:00.493 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:37:00.493 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:37:00.493 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:37:00.493 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:37:01.086 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:37:01.088 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 109 times 0:37:01.088 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:37:01.088 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:37:01.918 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 78 times 0:37:01.918 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:37:02.700 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:37:02.700 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:37:03.333 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 11 times 0:37:03.334 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:37:03.334 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:37:03.334 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:37:03.334 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:37:03.334 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:37:03.334 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:37:03.334 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:37:03.923 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:37:03.924 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 101 times 0:37:03.924 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:37:03.924 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:37:04.753 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 59 times 0:37:04.753 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:37:05.542 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:37:05.542 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:37:06.180 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 13 times 0:37:06.180 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:37:06.180 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:37:06.181 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:37:06.181 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:37:06.181 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:37:06.181 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:37:06.181 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:37:06.773 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:37:06.774 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 80 times 0:37:06.774 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:37:06.774 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:37:07.600 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 44 times 0:37:07.600 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:37:08.384 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:37:08.384 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:37:09.026 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 12 times 0:37:09.026 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:37:09.026 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:37:09.026 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:37:09.026 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:37:09.026 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:37:09.027 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:37:09.027 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:37:09.647 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:37:09.647 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1 times 0:37:09.647 20G / 46G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 12 0:37:09.648 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:37:09.648 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:37:09.648 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:37:09.648 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:37:09.648 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:37:09.648 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:37:09.648 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:37:09.648 20G / 46G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:37:09.648 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:37:10.238 20G / 46G INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 0:37:10.239 20G / 46G INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 0:37:10.239 20G / 46G INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 0:37:10.239 20G / 46G INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 0:37:10.239 20G / 46G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:37:10.239 20G / 46G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:37:10.239 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:37:11.347 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 488 times 0:37:11.348 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:37:12.102 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 15515 times 0:37:12.103 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:37:48.299 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 981 times 0:37:48.299 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:37:49.166 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 199 times 0:37:49.166 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:37:51.179 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 461393 times 0:37:51.200 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:37:51.832 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 541 times 0:37:51.833 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:37:52.429 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:37:52.429 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:37:54.232 20G / 46G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 140986 times 0:37:54.239 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:37:55.264 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 96 times 0:37:55.264 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:37:55.909 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 61 times 0:37:55.910 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:38:32.287 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 140 times 0:38:32.287 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:38:33.105 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 15 times 0:38:33.106 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:38:34.024 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 124 times 0:38:34.025 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:38:34.674 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 17 times 0:38:34.674 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:38:35.306 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:38:35.307 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:38:37.131 20G / 46G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 3 times 0:38:37.132 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:38:37.132 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 1 times 0:38:37.132 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:38:37.845 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 2 times 0:38:37.845 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:39:15.903 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 3 times 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 2 times 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 1 times 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 0:39:15.904 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:39:16.626 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 0:39:16.627 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:39:56.113 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 0:39:56.114 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:39:56.114 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:39:56.114 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:39:56.114 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 0:39:56.114 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:39:56.114 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:39:56.114 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:39:56.114 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:39:56.114 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:39:56.114 20G / 46G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:39:56.114 20G / 46G INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 0:40:02.226 20G / 46G INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 0:40:13.871 20G / 46G INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 8255512 times 0:40:13.981 20G / 46G INFO General (simplification.cpp : 491) Counting average coverage 0:40:14.682 20G / 46G INFO General (simplification.cpp : 497) Average coverage = 13.7284 0:40:14.682 20G / 46G INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:40:14.683 20G / 46G INFO General (read_converter.cpp : 102) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K49/simplified_contigs 0:40:14.687 20G / 46G INFO General (binary_converter.cpp : 96) 16384 reads processed 0:40:14.689 20G / 46G INFO General (binary_converter.cpp : 96) 32768 reads processed 0:40:14.692 20G / 46G INFO General (binary_converter.cpp : 96) 65536 reads processed 0:40:14.718 20G / 46G INFO General (binary_converter.cpp : 96) 131072 reads processed 0:40:14.786 20G / 46G INFO General (binary_converter.cpp : 96) 262144 reads processed 0:40:14.894 20G / 46G INFO General (binary_converter.cpp : 96) 524288 reads processed 0:40:15.128 20G / 46G INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:40:15.595 20G / 46G INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:40:15.692 20G / 46G INFO General (binary_converter.cpp : 111) 2260110 reads written 0:40:15.696 20G / 46G INFO General (pipeline.cpp : 287) SPAdes finished 0:40:17.487 1M / 46G INFO General (main.cpp : 136) Assembling time: 0 hours 40 minutes 17 seconds ===== K49 finished. ===== K73 started. == Running: /SPAdes-3.15.2-Linux/bin/spades-core /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/configs/config.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/configs/mda_mode.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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 148.098 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 0:00:01.047 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 845543 reads 0:00:01.893 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 1598530 reads 0:00:02.505 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 2135985 reads 0:00:03.263 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 2788682 reads 0:00:04.217 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 3352396 reads 0:00:05.106 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 3838556 reads 0:00:06.387 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 4649588 reads 0:00:07.598 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 5411989 reads 0:00:11.566 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 8444225 reads 0:00:25.289 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 16917228 reads 0:00:51.386 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 33792421 reads 0:01:41.689 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 67391973 reads 0:03:20.780 4641M / 4641M INFO General (kmer_splitters.hpp : 125) Processed 134587001 reads 0:05:54.864 1M / 4849M INFO General (kmer_splitters.hpp : 131) Used 194892048 reads 0:05:54.878 1M / 4849M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:06:46.467 1M / 6293M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 1708401242 kmers in total. 0:06:46.467 1M / 6293M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:06:46.483 1M / 6293M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:06:46.483 1M / 6293M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:06:46.483 1M / 6293M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:06:46.483 1M / 6293M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:06:46.483 1M / 6293M INFO General (kmer_splitter.hpp : 101) Using cell size of 279620 0:06:47.124 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 4401911 kmers 0:06:47.683 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 9166980 kmers 0:06:48.306 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 14721540 kmers 0:06:49.005 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 21764400 kmers 0:06:49.738 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 28528798 kmers 0:06:50.249 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 32472299 kmers 0:06:50.691 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 35791236 kmers 0:06:51.112 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 38937031 kmers 0:06:51.517 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 41975721 kmers 0:06:51.955 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 45110122 kmers 0:06:52.335 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 47886356 kmers 0:06:52.690 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 50466135 kmers 0:06:53.097 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 53528994 kmers 0:06:53.509 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 56689533 kmers 0:06:53.847 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 59035051 kmers 0:06:54.292 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 62389145 kmers 0:06:55.054 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 68122024 kmers 0:07:03.850 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 139040553 kmers 0:07:19.479 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 268608541 kmers 0:07:51.021 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 540880792 kmers 0:08:56.032 4641M / 6293M INFO General (kmer_splitters.hpp : 194) Processed 1075445051 kmers 0:10:15.775 4641M / 6293M INFO General (kmer_splitters.hpp : 199) Used 1708419282 kmers. 0:10:15.776 1M / 6293M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:11:00.645 1M / 9675M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 1711370930 kmers in total. 0:11:00.645 1M / 9675M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:11:34.061 1286M / 9675M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1711370930 kmers, 1236120168 bytes occupied (5.77839 bits per kmer). 0:11:34.061 1286M / 9675M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:12:44.899 2922M / 9675M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:16:27.921 2922M / 9675M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:16:28.003 2922M / 9675M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 0:16:28.003 2922M / 9675M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 0:17:38.593 8702M / 11G INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 53776640 0:17:38.634 2922M / 11G INFO Early A/T remover (early_simplification.hpp : 179) 53766459 74-mers were removed by early poly A/T remover 0:17:38.731 2922M / 11G INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 0:21:12.830 4202M / 11G INFO Early A/T remover (early_simplification.hpp : 330) Clipped tips: 10807316 0:21:12.830 2922M / 11G INFO Early A/T remover (early_simplification.hpp : 265) 270876519 74-mers were removed by early poly A/T tip clipper 0:21:13.079 2922M / 11G INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:21:13.082 2922M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:25:39.582 5515M / 13G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 48066459 sequences extracted 0:27:15.993 5515M / 14G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:27:45.863 5515M / 14G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 53 loops collected 0:27:46.973 5515M / 14G INFO General (debruijn_graph_constructor: 487) Total 96133024 edges to create 0:27:46.975 9215M / 14G INFO General (debruijn_graph_constructor: 489) Collecting link records 0:28:10.435 11G / 14G INFO General (debruijn_graph_constructor: 491) Ordering link records 0:28:11.693 11G / 14G INFO General (debruijn_graph_constructor: 493) Sorting done 0:28:12.148 11G / 14G INFO General (debruijn_graph_constructor: 503) Total 65375587 vertices to create 0:28:12.150 17G / 17G INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:29:03.826 15G / 19G INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:29:03.826 15G / 19G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:29:39.329 16G / 19G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1708401242 kmers, 1233975128 bytes occupied (5.77839 bits per kmer). 0:29:41.982 22G / 23G INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:33:27.482 22G / 23G INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:33:44.311 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 8000000 edges 0:34:00.829 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 16000000 edges 0:34:17.494 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 24000000 edges 0:34:34.088 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 32000000 edges 0:34:50.689 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 40000000 edges 0:35:07.281 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 48000000 edges 0:35:23.917 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 56000000 edges 0:35:40.981 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 64000000 edges 0:35:57.587 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 72000000 edges 0:36:14.114 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 80000000 edges 0:36:30.721 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 88000000 edges 0:36:47.284 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 96000000 edges 0:36:47.570 22G / 23G INFO General (coverage_filling.hpp : 82) Processed 96133008 edges 0:37:13.961 19G / 37G INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:37:24.142 19G / 37G INFO ThresholdFinder (ec_threshold_finder.hpp : 117) Bucket size: 5 0:37:24.153 19G / 37G INFO General (genomic_info_filler.cpp : 39) Average edge coverage: 3.32104 0:37:24.153 19G / 37G INFO General (genomic_info_filler.cpp : 40) Graph threshold: 141 0:37:24.155 19G / 37G INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 3.32104 0:37:24.155 19G / 37G INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:37:24.155 19G / 37G INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 0:37:24.164 19G / 37G INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:37:53.933 21G / 37G INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 83251425 out of 96133008, length: 18446744072012332655 0:38:00.746 22G / 37G INFO General (edge_index.hpp : 167) Using small index (max_id = 96613692) 0:38:11.029 22G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:42:06.733 23G / 37G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1384965400 kmers, 1000311808 bytes occupied (5.77812 bits per kmer). 0:42:08.597 33G / 37G INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:43:45.559 33G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:43:45.976 33G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:43:46.183 33G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:43:46.192 33G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:43:46.932 33G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:43:46.976 33G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:43:50.142 32G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:43:55.754 32G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:44:08.597 32G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 0:44:30.232 32G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 0:45:18.996 32G / 37G INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 0:46:23.341 35G / 37G INFO General (sequence_mapper_notifier.h: 95) Total 47592957 reads processed 0:47:05.685 23G / 38G INFO General (gap_closer.cpp : 452) Initializing gap closer 0:47:06.171 23G / 38G INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:48:49.549 23G / 38G INFO GapCloser (gap_closer.cpp : 393) Closing short gaps complete: filled 221383 gaps after checking 3021996 candidates 0:48:52.071 23G / 38G INFO General (gap_closer.cpp : 456) Gap closer done 0:48:57.872 19G / 38G INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:48:57.873 19G / 38G INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 0:48:57.873 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 0:48:59.260 19G / 38G INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 0:48:59.260 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 0:49:29.261 18G / 38G INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 16594554 times 0:49:29.418 18G / 38G INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 0:50:16.544 18G / 38G INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 32/703/38 0:50:16.545 18G / 38G INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 0/6/10 0:50:16.545 18G / 38G INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:50:16.545 18G / 38G INFO General (simplification.cpp : 368) Graph simplification started 0:50:16.546 18G / 38G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:50:16.546 18G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:50:16.546 18G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:50:16.546 18G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:02.766 18G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 10802191 times 0:51:03.243 18G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:06.799 18G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 424537 times 0:51:06.857 18G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:28.792 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 88419 times 0:51:28.808 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:29.116 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 3123 times 0:51:29.120 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:29.224 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 135 times 0:51:29.227 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:29.244 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 29 times 0:51:29.246 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:29.247 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:51:29.248 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:29.249 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:51:29.251 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:29.252 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:51:29.253 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:51:30.308 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:51:31.220 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 111762 times 0:51:31.232 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:51:31.234 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:32.892 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 42112 times 0:51:32.900 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:34.315 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 4926 times 0:51:34.318 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:36.215 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 2425 times 0:51:36.219 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:36.226 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 7 times 0:51:36.228 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:36.234 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:51:36.236 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:36.237 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 1 times 0:51:36.239 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:36.240 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:51:36.242 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:36.243 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:51:36.244 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:36.245 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:51:36.246 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:51:37.237 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:51:37.256 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1752 times 0:51:37.258 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:51:37.259 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:38.695 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 3858 times 0:51:38.697 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:40.085 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 84 times 0:51:40.088 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:41.222 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 220 times 0:51:41.225 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:41.227 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:51:41.228 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:41.230 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:51:41.232 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:41.233 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:51:41.234 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:51:42.220 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:51:42.229 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 538 times 0:51:42.231 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:51:42.232 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:43.658 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1040 times 0:51:43.661 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:45.054 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 2 times 0:51:45.057 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:46.131 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 61 times 0:51:46.133 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:46.135 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:51:46.137 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:46.138 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:51:46.140 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:46.141 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:51:46.142 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:51:47.121 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:51:47.127 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 292 times 0:51:47.128 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:51:47.130 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:48.530 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 469 times 0:51:48.534 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:49.925 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:51:49.929 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:50.991 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 31 times 0:51:50.994 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:50.995 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:51:50.997 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:50.998 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:51:51.000 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:51.001 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:51:51.002 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:51:51.980 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:51:51.985 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 166 times 0:51:51.987 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:51:51.988 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:53.382 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 235 times 0:51:53.386 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:54.779 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:51:54.782 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:55.832 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 8 times 0:51:55.835 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:55.837 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:51:55.838 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:55.839 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:51:55.841 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:51:55.842 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:51:55.843 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:51:56.829 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:51:56.834 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 119 times 0:51:56.836 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:51:56.837 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:51:58.259 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 147 times 0:51:58.262 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:51:59.658 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:51:59.662 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:00.716 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 15 times 0:52:00.719 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:00.720 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:52:00.722 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:52:00.723 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:52:00.724 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:00.726 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:52:00.727 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:52:01.705 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:52:01.710 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 86 times 0:52:01.711 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:52:01.712 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:03.130 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 98 times 0:52:03.134 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:52:04.523 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:52:04.526 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:05.575 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 9 times 0:52:05.578 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:05.579 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:52:05.581 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:52:05.582 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:52:05.583 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:05.584 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:52:05.586 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:52:06.568 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:52:06.572 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 63 times 0:52:06.574 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:52:06.575 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:07.997 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 83 times 0:52:08.000 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:52:09.396 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:52:09.400 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:10.451 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 6 times 0:52:10.454 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:10.455 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:52:10.457 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:52:10.458 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:52:10.459 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:10.461 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:52:10.462 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:52:11.443 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:52:11.447 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 53 times 0:52:11.449 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:52:11.450 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:12.881 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 46 times 0:52:12.884 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:52:14.273 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:52:14.276 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:15.325 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 1 times 0:52:15.328 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:15.329 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:52:15.331 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:52:15.332 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:52:15.333 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:15.334 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:52:15.336 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:52:16.316 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:52:16.321 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 40 times 0:52:16.322 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:52:16.323 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:17.737 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 31 times 0:52:17.741 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:52:19.133 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:52:19.136 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:20.192 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 1 times 0:52:20.195 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:20.196 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:52:20.197 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:52:20.199 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:52:20.200 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:20.201 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:52:20.202 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:52:21.183 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:52:21.187 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1 times 0:52:21.189 19G / 38G INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 12 0:52:21.190 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:52:21.192 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:52:21.193 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:52:21.194 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:52:21.195 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:52:21.197 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:52:21.198 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:52:21.199 19G / 38G INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:52:21.200 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:52:22.007 19G / 38G INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 0:52:22.017 19G / 38G INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:52:28.968 20G / 38G INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 29654386 out of 29984786, length: 1577743376 0:52:31.613 20G / 38G INFO General (edge_index.hpp : 167) Using small index (max_id = 96613692) 0:52:36.589 20G / 38G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:54:52.718 20G / 38G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 797639883 kmers, 576601920 bytes occupied (5.78308 bits per kmer). 0:54:53.443 26G / 38G INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:55:55.737 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:55:56.299 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:55:56.463 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:55:56.520 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:55:56.739 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:55:58.449 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:56:05.052 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:56:12.805 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:56:36.786 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 0:57:19.435 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 0:58:49.179 26G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 1:00:36.138 27G / 38G INFO General (sequence_mapper_notifier.h: 95) Total 47592957 reads processed 1:00:50.566 20G / 38G INFO General (gap_closer.cpp : 452) Initializing gap closer 1:00:50.974 20G / 38G INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 1:01:21.392 20G / 38G INFO GapCloser (gap_closer.cpp : 393) Closing short gaps complete: filled 6583 gaps after checking 1591796 candidates 1:01:22.240 20G / 38G INFO General (gap_closer.cpp : 456) Gap closer done 1:01:24.026 19G / 38G INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 1:01:24.104 19G / 38G INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 1:01:24.106 19G / 38G INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 1:01:24.107 19G / 38G INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 1:01:24.109 19G / 38G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:01:24.110 19G / 38G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 1:01:24.112 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 1:01:26.188 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 267 times 1:01:26.191 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 1:01:27.522 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 33339 times 1:01:27.528 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 1:02:24.311 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 309 times 1:02:24.313 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 1:02:25.707 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 776 times 1:02:25.710 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 1:02:28.418 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 321842 times 1:02:28.445 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 1:02:29.597 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 520 times 1:02:29.603 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 1:02:30.557 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 1:02:30.559 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 1:02:35.694 19G / 38G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 1709591 times 1:02:35.753 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 1:02:37.463 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 21 times 1:02:37.465 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 1:02:38.451 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 17 times 1:02:38.454 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 1:03:26.148 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 73 times 1:03:26.151 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 1:03:27.333 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 9 times 1:03:27.337 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 1:03:28.535 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 59 times 1:03:28.539 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 1:03:29.404 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 5 times 1:03:29.408 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 1:03:30.276 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 1:03:30.280 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 1:03:32.717 19G / 38G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 1:03:32.721 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 1:03:32.723 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 1:03:32.725 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 1:03:33.708 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 1 times 1:03:33.711 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 1:04:21.940 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 1 times 1:04:21.942 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 1:04:21.943 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 1:04:21.945 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 1:04:21.946 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 2 times 1:04:21.947 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 1:04:21.949 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 1:04:21.950 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 1:04:21.951 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 1:04:21.952 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 1:04:21.953 19G / 38G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 1:04:21.955 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 1:04:21.956 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 1:04:21.957 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 1:04:22.939 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 1:04:22.943 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 1:05:11.877 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 1:05:11.880 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 1:05:11.882 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 1:05:11.884 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 1:05:11.886 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 1:05:11.887 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 1:05:11.889 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 1:05:11.890 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 1:05:11.892 19G / 38G INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 1:05:11.894 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 1:05:11.895 19G / 38G INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 1:05:11.897 19G / 38G INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 1:05:20.558 19G / 38G INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 1:05:36.887 18G / 38G INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 10688549 times 1:05:37.067 18G / 38G INFO General (simplification.cpp : 491) Counting average coverage 1:05:37.908 18G / 38G INFO General (simplification.cpp : 497) Average coverage = 11.6091 1:05:37.911 18G / 38G INFO StageManager (stage.cpp : 185) STAGE == Mismatch Correction (id: mismatch_correction) 1:05:37.913 18G / 38G INFO General (graph_pack.cpp : 67) Index refill 1:05:37.914 18G / 38G INFO General (edge_index.hpp : 156) Using small index (max_id = 96613692) 1:05:39.489 18G / 38G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 1:06:14.854 18G / 38G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 278575756 kmers, 201481904 bytes occupied (5.78606 bits per kmer). 1:06:15.110 20G / 38G INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 1:06:32.704 20G / 38G INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 14375261 kmers to process 1:06:37.290 20G / 38G INFO General (graph_pack.cpp : 79) Normalizing done 1:06:37.293 20G / 38G INFO General (mismatch_correction.cpp : 400) Collect potential mismatches 1:06:40.810 20G / 38G INFO General (mismatch_correction.cpp : 193) Total 94888 edges (out of 4140298) with 433758 potential mismatch positions (4.57126 positions per edge) 1:06:40.824 20G / 38G INFO General (mismatch_correction.cpp : 402) Potential mismatches collected 1:06:43.495 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 1:06:43.530 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 1:06:43.615 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 1:06:44.242 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 1:06:44.569 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 1:06:45.378 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 1:06:47.979 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 1:06:54.221 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 1:07:04.098 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 1:07:24.180 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 1:08:08.779 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 1:09:33.231 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 67200000 reads 1:12:30.991 20G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 134400000 reads 1:16:13.056 21G / 38G INFO General (sequence_mapper_notifier.h: 95) Total 190371828 reads processed 1:16:17.269 20G / 38G INFO General (mismatch_correction.cpp : 395) All edges processed 1:16:17.317 20G / 38G INFO General (mismatch_correction.cpp : 450) Corrected 1764 nucleotides 1:16:17.328 20G / 38G INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 1:16:17.330 20G / 38G INFO General (contig_output.hpp : 16) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/before_rr.fasta 1:16:25.905 20G / 38G INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/assembly_graph_after_simplification.gfa 1:16:30.344 20G / 38G INFO StageManager (stage.cpp : 185) STAGE == Paired Information Counting (id: late_pair_info_count) 1:16:38.429 21G / 38G INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 14502701 kmers to process 1:16:43.005 21G / 38G INFO General (graph_pack.cpp : 79) Normalizing done 1:16:43.293 21G / 38G INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 500 1:16:43.297 21G / 38G INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 1:16:43.301 21G / 38G INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 1:16:43.317 21G / 38G INFO General (pair_info_count.cpp : 48) Selecting usual mapper 1:16:51.453 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 1:16:51.916 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 1:16:52.070 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 1:16:52.392 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 1:16:52.564 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 1:16:55.715 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 1:17:02.786 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 1:17:13.310 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 1:17:42.778 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 1:18:34.976 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 1:20:25.769 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 1:22:46.725 21G / 38G INFO General (sequence_mapper_notifier.h: 95) Total 47592957 reads processed 1:22:46.965 21G / 38G INFO General (pair_info_count.cpp : 220) Edge pairs: 2097958 1:22:46.969 21G / 38G INFO General (pair_info_count.cpp : 224) 3726218 paired reads (7.82935% of all) aligned to long edges 1:22:46.973 21G / 38G INFO General (pair_info_count.cpp : 373) Insert size = 238.589, deviation = 66.1323, left quantile = 166, right quantile = 327, read length = 150 1:22:46.976 21G / 38G INFO General (pair_info_count.cpp : 402) Mapping library #0 1:22:46.979 21G / 38G INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 1:22:46.982 21G / 38G INFO General (pair_info_count.cpp : 302) Left insert size quantile 166, right insert size quantile 327, filtering threshold 0, rounding threshold 0 1:22:46.997 21G / 38G INFO General (pair_info_count.cpp : 48) Selecting usual mapper 1:22:54.684 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 1:22:54.945 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 1:22:55.411 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 1:22:55.611 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 1:22:55.681 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 1:22:58.736 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 1:23:05.794 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 1:23:15.892 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 1:23:44.507 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 1:24:36.597 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 1:26:24.979 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 1:28:40.976 21G / 38G INFO General (sequence_mapper_notifier.h: 95) Total 47592957 reads processed 1:28:41.645 21G / 38G INFO General (pair_info_count.cpp : 411) Mapping single reads of library #0 1:28:41.651 21G / 38G INFO General (pair_info_count.cpp : 266) Will calculate lib coverage as well 1:28:41.655 21G / 38G INFO General (pair_info_count.cpp : 48) Selecting usual mapper 1:28:44.546 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 1:28:44.951 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 1:28:45.482 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 1:28:45.750 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 1:28:46.683 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 1:28:46.706 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 1:28:50.121 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 1:28:57.340 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 1:29:08.200 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 8400000 reads 1:29:35.355 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 16800000 reads 1:30:25.831 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 33600000 reads 1:32:14.749 21G / 38G INFO General (sequence_mapper_notifier.h: 77) Processed 67200000 reads 1:34:31.389 22G / 38G INFO General (sequence_mapper_notifier.h: 95) Total 95185914 reads processed 1:34:31.816 22G / 38G INFO General (pair_info_count.cpp : 413) Total paths obtained from single reads: 0 1:34:31.821 22G / 38G INFO StageManager (stage.cpp : 185) STAGE == Distance Estimation (id: distance_estimation) 1:34:31.825 22G / 38G INFO General (distance_estimation.cpp : 179) Processing library #0 1:34:31.829 22G / 38G INFO General (distance_estimation.cpp : 150) Weight Filter Done 1:34:31.832 22G / 38G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 1:34:35.725 22G / 38G INFO General (distance_estimation.cpp : 37) Filtering info 1:34:35.849 22G / 38G INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 4209564 1:34:38.072 21G / 38G INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 2367168 1:34:38.140 21G / 38G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 1:34:38.970 21G / 38G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 1:34:38.977 21G / 38G INFO General (distance_estimation.cpp : 160) Improving paired information 1:34:43.953 21G / 38G INFO PairInfoImprover (pair_info_improver.hpp : 105) Paired info stats: missing = 605; contradictional = 0 1:34:48.933 21G / 38G INFO PairInfoImprover (pair_info_improver.hpp : 105) Paired info stats: missing = 7; contradictional = 0 1:34:48.942 21G / 38G INFO StageManager (stage.cpp : 185) STAGE == Repeat Resolving (id: repeat_resolving) 1:34:48.949 21G / 38G INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 1:34:48.954 21G / 38G INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 1:34:56.136 30G / 38G INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 1:34:56.145 30G / 38G INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2368392 1:34:56.163 30G / 38G INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 2368392 1:34:56.629 31G / 38G INFO General (extenders_logic.cpp : 543) Using 1 paired-end library 1:34:56.640 31G / 38G INFO General (extenders_logic.cpp : 544) Using 1 paired-end scaffolding library 1:34:56.650 31G / 38G INFO General (extenders_logic.cpp : 545) Using 0 single read libraries 1:34:56.659 31G / 38G INFO General (launcher.cpp : 447) Total number of extenders is 5 1:34:56.669 31G / 38G INFO General (path_extenders.cpp : 36) Processed 0 paths from 2067681 (0%) 1:34:56.815 31G / 38G INFO General (path_extenders.cpp : 34) Processed 128 paths from 2067681 (0%) 1:34:56.972 31G / 38G INFO General (path_extenders.cpp : 34) Processed 256 paths from 2067681 (0%) 1:34:57.002 31G / 38G INFO General (path_extenders.cpp : 34) Processed 512 paths from 2067681 (0%) 1:34:57.184 31G / 38G INFO General (path_extenders.cpp : 34) Processed 1024 paths from 2067681 (0%) 1:34:57.376 31G / 38G INFO General (path_extenders.cpp : 34) Processed 2048 paths from 2067681 (0%) 1:34:57.597 31G / 38G INFO General (path_extenders.cpp : 34) Processed 4096 paths from 2067681 (0%) 1:34:58.298 31G / 38G INFO General (path_extenders.cpp : 34) Processed 8192 paths from 2067681 (0%) 1:34:58.774 31G / 38G INFO General (path_extenders.cpp : 34) Processed 16384 paths from 2067681 (0%) 1:34:59.901 31G / 38G INFO General (path_extenders.cpp : 34) Processed 32768 paths from 2067681 (1%) 1:35:01.589 31G / 38G INFO General (path_extenders.cpp : 34) Processed 65536 paths from 2067681 (3%) 1:35:04.539 32G / 38G INFO General (path_extenders.cpp : 34) Processed 131072 paths from 2067681 (6%) 1:35:07.572 32G / 38G INFO General (path_extenders.cpp : 36) Processed 206769 paths from 2067681 (10%) 1:35:09.474 32G / 38G INFO General (path_extenders.cpp : 34) Processed 262144 paths from 2067681 (12%) 1:35:14.427 33G / 38G INFO General (path_extenders.cpp : 36) Processed 413538 paths from 2067681 (20%) 1:35:22.795 33G / 38G INFO General (path_extenders.cpp : 34) Processed 524288 paths from 2067681 (25%) 1:35:32.058 34G / 38G INFO General (path_extenders.cpp : 36) Processed 620307 paths from 2067681 (30%) 1:35:36.636 34G / 38G INFO General (path_extenders.cpp : 36) Processed 827076 paths from 2067681 (40%) 1:35:42.203 35G / 38G INFO General (path_extenders.cpp : 36) Processed 1033845 paths from 2067681 (50%) 1:35:42.986 35G / 38G INFO General (path_extenders.cpp : 34) Processed 1048576 paths from 2067681 (50%) 1:35:55.419 36G / 38G INFO General (path_extenders.cpp : 36) Processed 1240614 paths from 2067681 (60%) 1:37:23.428 37G / 38G INFO General (path_extenders.cpp : 36) Processed 1447383 paths from 2067681 (70%) 1:37:53.898 38G / 38G INFO General (path_extenders.cpp : 36) Processed 1654152 paths from 2067681 (80%) 1:38:18.503 38G / 39G INFO General (path_extenders.cpp : 36) Processed 1860921 paths from 2067681 (90%) 1:45:21.954 39G / 40G INFO General (launcher.cpp : 250) Finalizing paths 1:45:21.968 39G / 40G INFO General (launcher.cpp : 252) Deduplicating paths 1:45:33.950 39G / 40G INFO General (launcher.cpp : 256) Paths deduplicated 1:45:33.965 39G / 40G INFO General (launcher.cpp : 263) Overlaps will not be removed 1:45:37.251 39G / 40G INFO General (launcher.cpp : 273) Paths finalized 1:45:37.266 39G / 40G INFO General (launcher.cpp : 454) Closing gaps in paths 1:45:42.523 46G / 47G INFO General (launcher.cpp : 484) Gap closing completed 1:45:43.736 46G / 47G INFO General (launcher.cpp : 302) Traversing tandem repeats 1:45:56.618 46G / 47G INFO General (launcher.cpp : 312) Traversed 0 loops 1:45:56.635 46G / 47G INFO General (launcher.cpp : 250) Finalizing paths 1:45:56.653 46G / 47G INFO General (launcher.cpp : 252) Deduplicating paths 1:46:06.458 46G / 47G INFO General (launcher.cpp : 256) Paths deduplicated 1:46:06.475 46G / 47G INFO General (launcher.cpp : 263) Overlaps will not be removed 1:46:08.759 46G / 47G INFO General (launcher.cpp : 273) Paths finalized 1:46:08.776 46G / 47G INFO General (launcher.cpp : 499) Finalizing paths - hard 1:46:12.383 53G / 54G INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 152 1:46:12.403 53G / 54G INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 152 1:46:12.423 53G / 54G INFO General (launcher.cpp : 297) Length cutoff: 152 1:46:12.918 49G / 54G INFO General (launcher.cpp : 295) Read length relative cutoff 2 converted to 227 1:46:13.117 49G / 54G INFO General (launcher.cpp : 296) Read length absolute cutoff 180 bp converted to 227 1:46:13.134 49G / 54G INFO General (launcher.cpp : 297) Length cutoff: 227 1:46:13.258 49G / 54G INFO General (launcher.cpp : 295) Read length relative cutoff 2 converted to 227 1:46:13.278 49G / 54G INFO General (launcher.cpp : 296) Read length absolute cutoff 180 bp converted to 227 1:46:13.298 49G / 54G INFO General (launcher.cpp : 297) Length cutoff: 227 1:46:17.670 46G / 54G INFO General (launcher.cpp : 499) Finalizing paths - soft 1:46:20.798 53G / 54G INFO General (launcher.cpp : 295) Read length relative cutoff 1.05 converted to 84 1:46:20.819 53G / 54G INFO General (launcher.cpp : 296) Read length absolute cutoff 85 bp converted to 84 1:46:20.840 53G / 54G INFO General (launcher.cpp : 297) Length cutoff: 84 1:46:21.013 52G / 54G INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 152 1:46:21.083 52G / 54G INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 152 1:46:21.102 52G / 54G INFO General (launcher.cpp : 297) Length cutoff: 152 1:46:21.238 52G / 54G INFO General (launcher.cpp : 295) Read length relative cutoff 1.2 converted to 107 1:46:21.258 52G / 54G INFO General (launcher.cpp : 296) Read length absolute cutoff 100 bp converted to 107 1:46:21.278 52G / 54G INFO General (launcher.cpp : 297) Length cutoff: 107 1:46:33.089 46G / 54G INFO General (launcher.cpp : 507) Finalizing main paths 1:46:33.343 46G / 54G INFO General (launcher.cpp : 295) Read length relative cutoff 1.3 converted to 122 1:46:33.361 46G / 54G INFO General (launcher.cpp : 296) Read length absolute cutoff 110 bp converted to 122 1:46:33.379 46G / 54G INFO General (launcher.cpp : 297) Length cutoff: 122 1:46:33.792 44G / 54G INFO General (launcher.cpp : 295) Read length relative cutoff 1.6 converted to 167 1:46:33.813 44G / 54G INFO General (launcher.cpp : 296) Read length absolute cutoff 140 bp converted to 167 1:46:33.831 44G / 54G INFO General (launcher.cpp : 297) Length cutoff: 167 1:46:34.035 44G / 54G INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 152 1:46:34.053 44G / 54G INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 152 1:46:34.071 44G / 54G INFO General (launcher.cpp : 297) Length cutoff: 152 1:46:35.698 43G / 54G INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 1:46:40.055 25G / 54G INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 1:46:40.175 25G / 54G INFO General (contig_output.hpp : 16) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/before_rr.fasta 1:46:48.813 25G / 54G INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/assembly_graph_with_scaffolds.gfa 1:46:53.257 25G / 54G INFO General (contig_output_stage.cpp : 165) Outputting FastG graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/assembly_graph.fastg 1:47:12.536 26G / 54G INFO General (contig_output_stage.cpp : 98) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/transcripts.fasta 1:47:14.166 26G / 54G INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/transcripts.paths 1:47:15.696 26G / 54G INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 1:47:17.135 25G / 54G INFO General (pipeline.cpp : 287) SPAdes finished 1:47:23.516 1M / 54G INFO General (main.cpp : 136) Assembling time: 1 hours 47 minutes 23 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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/before_rr.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/before_rr.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/assembly_graph_after_simplification.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/assembly_graph_after_simplification.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/transcripts.paths /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/transcripts.paths /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/assembly_graph_with_scaffolds.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/assembly_graph_with_scaffolds.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/assembly_graph.fastg /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/assembly_graph.fastg /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/hard_filtered_final_paths.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/hard_filtered_transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/K73/soft_filtered_final_paths.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/scaffolds.fasta --misc_dir /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/transcripts.paths * Hard filtered transcripts are in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/hard_filtered_transcripts.fasta * Soft filtered transcripts are in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/soft_filtered_transcripts.fasta * Assembly graph is in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metaT/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/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/12596608-3dfe-424c-9e2d-e42adac8492c/call-asse/metatranscriptome_assy/c328deff-697a-40bb-bd94-0f520b0236eb/call-assy/execution/out.spades/spades.log Thank you for using SPAdes!