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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades --12 /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/reads.input.fastq.gz System information: SPAdes version: 3.15.2 Python version: 3.9.16 OS: Linux-5.14.21-150400.24.111_12.0.91-cray_shasta_c-x86_64-with-glibc2.34 Output dir: /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/spades.log /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/reads.input.fastq.gz: max reads length: 300 Reads length: 300 Auto K value (149) is too large, all K values should not exceed 127. Setting k=127. K values to be used: [55, 127] ===== Before start started. ===== Preprocess reads started. ===== Preprocess reads finished. ===== Assembling started. ===== K55 started. == Running: /SPAdes-3.15.2-Linux/bin/spades-core /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K55/configs/config.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K55/configs/mda_mode.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K55/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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K55/configs/config.info 0:00:00.013 1M / 16M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K55/configs/mda_mode.info 0:00:00.013 1M / 16M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K55/configs/rna_mode.info 0:00:00.013 1M / 16M INFO General (memory_limit.cpp : 48) Memory limit set to 120 Gb 0:00:00.013 1M / 16M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.2, git revision aab988a9b4986906b38396da7233bb1ee02982f2 0:00:00.013 1M / 16M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.013 1M / 16M INFO General (main.cpp : 109) Assembling dataset (/pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/dataset.info) with K=55 0:00:00.013 1M / 16M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 8 0:00:00.013 1M / 16M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.013 1M / 16M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.013 1M / 16M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.013 1M / 16M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.013 1M / 16M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.013 1M / 16M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:00.013 1M / 16M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 0:00:00.013 1M / 16M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.015 1M / 16M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.015 1M / 16M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.384 14M / 57M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:00.398 14M / 60M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:00.629 14M / 98M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:00.870 14M / 140M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:01.595 14M / 188M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:02.810 14M / 251M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:00:05.317 14M / 285M INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:00:11.323 14M / 348M INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:00:13.814 14M / 351M INFO General (binary_converter.cpp : 111) 2487008 reads written 0:00:13.814 7M / 351M INFO General (read_converter.cpp : 81) Converting single reads 0:00:13.816 11M / 351M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:13.816 7M / 351M INFO General (read_converter.cpp : 87) Converting merged reads 0:00:13.817 11M / 351M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:13.831 1M / 351M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:00:13.839 1M / 351M INFO General (construction.cpp : 153) Max read length 300 0:00:13.839 1M / 351M INFO General (construction.cpp : 159) Average read length 296.191 0:00:13.839 1M / 351M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:00:13.841 1M / 351M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:00:13.842 1M / 351M INFO General (file_limit.hpp : 32) Open file limit set to 500000 0:00:13.842 1M / 351M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:00:13.842 1M / 351M INFO General (kmer_splitter.hpp : 101) Using cell size of 419430 0:00:20.012 4641M / 5196M INFO General (kmer_splitters.hpp : 125) Processed 1961419 reads 0:00:26.086 4641M / 5376M INFO General (kmer_splitters.hpp : 125) Processed 3979737 reads 0:00:32.198 4641M / 5376M INFO General (kmer_splitters.hpp : 125) Processed 5925881 reads 0:00:38.390 4641M / 5384M INFO General (kmer_splitters.hpp : 125) Processed 7925109 reads 0:00:41.872 4641M / 5384M INFO General (kmer_splitters.hpp : 125) Processed 9022654 reads 0:00:42.959 4641M / 5384M INFO General (kmer_splitters.hpp : 125) Processed 9250863 reads 0:00:44.220 4641M / 5384M INFO General (kmer_splitters.hpp : 125) Processed 9501948 reads 0:00:45.526 4641M / 5384M INFO General (kmer_splitters.hpp : 125) Processed 9760737 reads 0:00:46.529 4641M / 5384M INFO General (kmer_splitters.hpp : 125) Processed 9948032 reads 0:00:46.530 1M / 5384M INFO General (kmer_splitters.hpp : 131) Used 9948032 reads 0:00:46.539 1M / 5384M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:00:52.239 1M / 5384M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 662026801 kmers in total. 0:00:52.239 1M / 5384M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:00:52.253 1M / 5384M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:00:52.253 1M / 5384M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:00:52.253 1M / 5384M INFO General (file_limit.hpp : 32) Open file limit set to 500000 0:00:52.253 1M / 5384M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:00:52.253 1M / 5384M INFO General (kmer_splitter.hpp : 101) Using cell size of 419430 0:00:53.365 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 11380982 kmers 0:00:54.216 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 24619392 kmers 0:00:55.168 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 38876348 kmers 0:00:56.074 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 52562109 kmers 0:00:56.933 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 64730260 kmers 0:00:57.767 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 77460162 kmers 0:00:58.662 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 90712561 kmers 0:00:59.643 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 104955305 kmers 0:01:00.579 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 118659200 kmers 0:01:01.399 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 130813414 kmers 0:01:02.242 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 143676194 kmers 0:01:03.138 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 156921758 kmers 0:01:04.143 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 171162417 kmers 0:01:05.133 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 184874930 kmers 0:01:05.961 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 197032240 kmers 0:01:06.800 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 209881741 kmers 0:01:07.682 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 223138630 kmers 0:01:08.714 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 237396770 kmers 0:01:11.339 4641M / 5384M INFO General (kmer_splitters.hpp : 194) Processed 276098608 kmers 0:01:29.232 4641M / 6459M INFO General (kmer_splitters.hpp : 194) Processed 540887824 kmers 0:01:37.639 4641M / 7324M INFO General (kmer_splitters.hpp : 199) Used 662029001 kmers. 0:01:37.640 1M / 7324M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:01:50.097 1M / 7702M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 661299890 kmers in total. 0:01:50.097 1M / 7702M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:01:59.829 465M / 7702M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 661299890 kmers, 477690968 bytes occupied (5.77881 bits per kmer). 0:01:59.830 465M / 7702M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:02:17.802 1097M / 7702M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:03:48.181 1097M / 7702M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:03:48.507 1097M / 7702M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 0:03:48.507 1097M / 7702M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 0:04:03.268 1103M / 7702M INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 59040 0:04:03.268 1097M / 7702M INFO Early A/T remover (early_simplification.hpp : 179) 58703 56-mers were removed by early poly A/T remover 0:04:03.389 1097M / 7702M INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 0:04:58.982 1098M / 7702M INFO Early A/T remover (early_simplification.hpp : 330) Clipped tips: 13611 0:04:58.982 1097M / 7702M INFO Early A/T remover (early_simplification.hpp : 265) 361694 56-mers were removed by early poly A/T tip clipper 0:04:59.304 1097M / 7702M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:04:59.306 1097M / 7702M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:06:48.139 1694M / 7702M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 9817115 sequences extracted 0:07:38.081 1694M / 7702M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:07:46.315 1695M / 7702M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 30 loops collected 0:07:46.603 1694M / 7702M INFO General (debruijn_graph_constructor: 487) Total 19634290 edges to create 0:07:46.604 2453M / 7702M INFO General (debruijn_graph_constructor: 489) Collecting link records 0:07:51.773 2753M / 7702M INFO General (debruijn_graph_constructor: 491) Ordering link records 0:07:51.991 2753M / 7702M INFO General (debruijn_graph_constructor: 493) Sorting done 0:07:52.087 2882M / 7702M INFO General (debruijn_graph_constructor: 503) Total 9113205 vertices to create 0:07:52.087 3724M / 7702M INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:08:00.058 3147M / 7702M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:08:00.058 3147M / 7702M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:08:09.451 3611M / 7702M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 662026801 kmers, 478215600 bytes occupied (5.77881 bits per kmer). 0:08:09.818 6139M / 7702M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:09:03.930 6139M / 7702M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:09:34.561 6139M / 7702M INFO General (coverage_filling.hpp : 82) Processed 8000000 edges 0:10:06.381 6139M / 7702M INFO General (coverage_filling.hpp : 82) Processed 16000000 edges 0:10:20.750 6139M / 7702M INFO General (coverage_filling.hpp : 82) Processed 19623100 edges 0:10:26.231 2064M / 7702M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:10:28.644 2065M / 7702M INFO ThresholdFinder (ec_threshold_finder.hpp : 117) Bucket size: 5 0:10:28.644 2065M / 7702M INFO General (genomic_info_filler.cpp : 39) Average edge coverage: 1.80832 0:10:28.644 2065M / 7702M INFO General (genomic_info_filler.cpp : 40) Graph threshold: 98 0:10:28.645 2064M / 7702M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 1.80832 0:10:28.645 2064M / 7702M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:10:28.645 2064M / 7702M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 0:10:28.658 2073M / 7702M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:10:30.097 2217M / 7702M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 6637196 out of 19623100, length: 884737188 0:10:30.708 2290M / 7702M INFO General (edge_index.hpp : 167) Using small index (max_id = 19732464) 0:10:33.264 2290M / 7702M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:11:48.357 2656M / 7702M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 525777921 kmers, 379751352 bytes occupied (5.77813 bits per kmer). 0:11:48.830 6668M / 8062M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:12:25.348 6683M / 8064M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:12:25.449 6698M / 8064M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:12:25.672 6733M / 8064M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:12:26.136 6763M / 8064M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:12:39.171 6769M / 8097M INFO General (sequence_mapper_notifier.h: 77) Processed 1443408 reads 0:12:41.415 6701M / 8097M INFO General (sequence_mapper_notifier.h: 77) Processed 1643408 reads 0:12:43.535 6703M / 8097M INFO General (sequence_mapper_notifier.h: 77) Processed 2154308 reads 0:12:55.828 6792M / 8097M INFO General (sequence_mapper_notifier.h: 95) Total 2487008 reads processed 0:12:57.855 2387M / 8109M INFO General (gap_closer.cpp : 452) Initializing gap closer 0:12:57.927 2387M / 8109M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:13:12.291 2387M / 8109M INFO GapCloser (gap_closer.cpp : 393) Closing short gaps complete: filled 66 gaps after checking 1655025 candidates 0:13:12.466 2387M / 8109M INFO General (gap_closer.cpp : 456) Gap closer done 0:13:12.892 2065M / 8109M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:13:12.892 2065M / 8109M INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 0:13:12.892 2065M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 0:13:13.224 2065M / 8109M INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 0:13:13.225 2065M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 0:13:14.255 2062M / 8109M INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 108574 times 0:13:14.261 2062M / 8109M INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 0:13:25.971 2020M / 8109M INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 0/358/68 0:13:25.983 2020M / 8109M INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 6/1563/775975 0:13:25.983 2017M / 8109M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:13:25.983 2017M / 8109M INFO General (simplification.cpp : 368) Graph simplification started 0:13:25.983 2017M / 8109M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:13:25.983 2017M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:13:25.983 2017M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:13:25.983 2017M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:13:29.858 1988M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 646854 times 0:13:29.884 1988M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:13:31.333 1980M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 334522 times 0:13:31.341 1980M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:21.601 3471M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 227780 times 0:14:21.612 3471M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:22.304 3435M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 439 times 0:14:22.307 3435M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:23.024 3398M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 6871 times 0:14:23.027 3398M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:23.055 3375M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 63 times 0:14:23.058 3375M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:23.062 3375M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 0:14:23.064 3375M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:23.066 3375M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:23.068 3375M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:23.070 3375M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:23.072 3375M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:23.074 3375M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:23.076 3375M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:23.078 3375M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:23.080 3375M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:23.082 3375M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:23.084 3375M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:24.154 3443M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:37.291 3398M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1536690 times 0:14:37.344 3398M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:14:37.346 3398M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:37.673 3361M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 14495 times 0:14:37.677 3361M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:38.052 3323M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 29040 times 0:14:38.057 3323M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:41.066 3336M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 8944 times 0:14:41.090 3336M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:41.118 3335M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 3 times 0:14:41.122 3335M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:41.135 3334M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 1 times 0:14:41.138 3334M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:41.141 3334M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:41.143 3334M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:41.145 3334M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:41.147 3334M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:41.149 3334M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:41.152 3334M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:41.154 3334M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:41.156 3334M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:41.332 3266M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:41.368 3266M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 3656 times 0:14:41.371 3266M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:14:41.374 3266M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:41.617 3266M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1835 times 0:14:41.621 3266M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:41.876 3265M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 2860 times 0:14:41.879 3265M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:42.400 3265M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 192 times 0:14:42.404 3265M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:42.408 3265M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:42.410 3265M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:42.412 3265M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:42.415 3265M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:42.417 3265M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:42.419 3265M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:42.595 3264M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:42.605 3264M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 792 times 0:14:42.608 3264M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:14:42.610 3264M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:42.847 3264M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 369 times 0:14:42.851 3264M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:43.095 3264M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 249 times 0:14:43.098 3264M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:43.566 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 41 times 0:14:43.569 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:43.572 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:43.574 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:43.576 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:43.579 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:43.581 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:43.583 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:43.758 3268M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:43.764 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 380 times 0:14:43.767 3268M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:14:43.769 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:44.003 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 53 times 0:14:44.009 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:44.246 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 21 times 0:14:44.251 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:44.702 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 26 times 0:14:44.705 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:44.707 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:44.710 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:44.712 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:44.714 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:44.716 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:44.718 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:44.896 3268M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:44.901 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 228 times 0:14:44.903 3268M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:14:44.906 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:45.142 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 20 times 0:14:45.147 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:45.385 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 2 times 0:14:45.390 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:45.829 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 9 times 0:14:45.832 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:45.834 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:45.837 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:45.839 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:45.841 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:45.844 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:45.846 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:46.019 3269M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:46.024 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 153 times 0:14:46.026 3269M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:14:46.029 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:46.266 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 8 times 0:14:46.272 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:46.515 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:46.520 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:46.958 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 8 times 0:14:46.961 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:46.964 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:46.966 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:46.968 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:46.970 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:46.972 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:46.975 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:47.148 3269M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:47.153 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 104 times 0:14:47.155 3269M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:14:47.157 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:47.394 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 6 times 0:14:47.399 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:47.637 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:47.643 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:48.083 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 3 times 0:14:48.087 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:48.089 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:48.091 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:48.094 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:48.096 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:48.098 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:48.100 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:48.275 3269M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:48.280 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 89 times 0:14:48.282 3269M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:14:48.284 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:48.522 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:14:48.527 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:48.774 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:48.779 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:49.223 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 6 times 0:14:49.227 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:49.229 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:49.231 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:49.233 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:49.236 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:49.238 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:49.240 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:49.412 3269M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:49.415 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 61 times 0:14:49.418 3269M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:14:49.420 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:49.656 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:14:49.662 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:49.900 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:49.904 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:50.337 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 1 times 0:14:50.341 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:50.343 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:50.346 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:50.348 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:50.350 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:50.352 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:50.354 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:50.527 3269M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:50.531 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 52 times 0:14:50.533 3269M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:14:50.535 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:50.772 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:14:50.776 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:51.015 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:51.020 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:51.453 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 2 times 0:14:51.456 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:51.458 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:51.461 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:51.463 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:51.465 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:51.467 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:51.469 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:51.642 3269M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:51.645 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:14:51.647 3269M / 8109M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 12 0:14:51.649 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:51.652 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:14:51.654 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:51.656 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:14:51.658 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:14:51.660 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:14:51.663 3269M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:14:51.665 3269M / 8109M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:51.667 3269M / 8109M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:14:51.788 3262M / 8109M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 0:14:51.800 3271M / 8109M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:14:53.048 3415M / 8109M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 4427750 out of 4986334, length: 780754764 0:14:53.439 3451M / 8109M INFO General (edge_index.hpp : 167) Using small index (max_id = 19732464) 0:14:55.260 3451M / 8109M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:15:49.413 3731M / 8109M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 400417163 kmers, 289210482 bytes occupied (5.77818 bits per kmer). 0:15:49.779 6787M / 8109M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:16:46.099 6817M / 8109M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:16:46.592 6842M / 8109M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:16:46.718 6888M / 8109M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:16:48.833 6922M / 8109M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:16:53.684 6888M / 8109M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:17:01.567 6891M / 8109M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:17:27.989 7021M / 8109M INFO General (sequence_mapper_notifier.h: 95) Total 2487008 reads processed 0:17:31.173 3705M / 8109M INFO General (gap_closer.cpp : 452) Initializing gap closer 0:17:31.331 3705M / 8109M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:17:35.531 3705M / 8109M INFO GapCloser (gap_closer.cpp : 393) Closing short gaps complete: filled 77 gaps after checking 724045 candidates 0:17:35.653 3705M / 8109M INFO General (gap_closer.cpp : 456) Gap closer done 0:17:36.144 3262M / 8109M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 0:17:36.162 3262M / 8109M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 0:17:36.165 3262M / 8109M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 0:17:36.167 3262M / 8109M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 0:17:36.169 3262M / 8109M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:17:36.171 3262M / 8109M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:17:36.173 3262M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:17:36.523 3262M / 8109M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 197 times 0:17:36.529 3262M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:17:36.847 3261M / 8109M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 4599 times 0:17:36.851 3261M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:17:45.013 3267M / 8109M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 305 times 0:17:45.018 3267M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:17:45.250 3267M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 21 times 0:17:45.255 3267M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:17:45.758 3268M / 8109M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 49253 times 0:17:45.766 3268M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:17:46.253 3274M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 319 times 0:17:46.258 3274M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:17:46.654 3278M / 8109M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:17:46.657 3278M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:17:46.919 3278M / 8109M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 817 times 0:17:46.923 3278M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:17:47.280 3277M / 8109M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 201 times 0:17:47.284 3277M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:17:47.549 3277M / 8109M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 23 times 0:17:47.554 3277M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:17:55.508 3277M / 8109M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 19 times 0:17:55.510 3277M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:17:55.733 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 97 times 0:17:55.739 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:17:55.967 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 255 times 0:17:55.972 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:17:56.375 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 7 times 0:17:56.379 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:17:56.771 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:17:56.775 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:17:57.036 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 2 times 0:17:57.040 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:17:57.043 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 0:17:57.045 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:17:57.319 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 0:17:57.324 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:18:05.522 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 0:18:05.526 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:18:05.529 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:18:05.531 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:18:05.533 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 0:18:05.536 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:18:05.538 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:18:05.540 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:18:05.542 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:18:05.544 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:18:05.546 3276M / 8109M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:18:05.548 3276M / 8109M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 0:18:07.013 3276M / 8109M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 0:18:09.665 3164M / 8109M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 1729685 times 0:18:09.683 3139M / 8109M INFO General (simplification.cpp : 491) Counting average coverage 0:18:09.924 3139M / 8109M INFO General (simplification.cpp : 497) Average coverage = 5.56617 0:18:09.928 3139M / 8109M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:18:09.931 3139M / 8109M INFO General (read_converter.cpp : 102) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K55/simplified_contigs 0:18:09.937 3142M / 8109M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:18:09.941 3142M / 8109M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:18:09.949 3142M / 8109M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:18:09.978 3142M / 8109M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:18:10.049 3142M / 8109M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:18:10.186 3142M / 8109M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:18:10.283 3142M / 8109M INFO General (binary_converter.cpp : 111) 658189 reads written 0:18:10.289 3139M / 8109M INFO General (pipeline.cpp : 287) SPAdes finished 0:18:13.615 1M / 8109M INFO General (main.cpp : 136) Assembling time: 0 hours 18 minutes 13 seconds ===== K55 finished. ===== K127 started. == Running: /SPAdes-3.15.2-Linux/bin/spades-core /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/configs/config.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/configs/mda_mode.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/configs/rna_mode.info 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/configs/config.info 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/configs/mda_mode.info 0:00:00.000 1M / 19M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/configs/rna_mode.info 0:00:00.000 1M / 19M INFO General (memory_limit.cpp : 48) Memory limit set to 120 Gb 0:00:00.000 1M / 19M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.2, git revision aab988a9b4986906b38396da7233bb1ee02982f2 0:00:00.000 1M / 19M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.000 1M / 19M INFO General (main.cpp : 109) Assembling dataset (/pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/dataset.info) with K=127 0:00:00.000 1M / 19M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 8 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.000 1M / 19M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.000 1M / 19M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:00.000 1M / 19M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 0:00:00.000 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.001 1M / 19M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.002 1M / 19M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:00:00.002 1M / 19M INFO General (construction.cpp : 118) Contigs from previous K will be used: /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K55/simplified_contigs 0:00:00.004 1M / 19M INFO General (construction.cpp : 153) Max read length 300 0:00:00.004 1M / 19M INFO General (construction.cpp : 159) Average read length 296.191 0:00:00.004 1M / 19M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:00:00.004 1M / 19M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:00:00.005 1M / 19M INFO General (file_limit.hpp : 32) Open file limit set to 500000 0:00:00.005 1M / 19M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:00:00.005 1M / 19M INFO General (kmer_splitter.hpp : 101) Using cell size of 209715 0:00:04.830 4641M / 5538M INFO General (kmer_splitters.hpp : 125) Processed 1529390 reads 0:00:09.420 4641M / 5538M INFO General (kmer_splitters.hpp : 125) Processed 3067727 reads 0:00:14.068 4641M / 5704M INFO General (kmer_splitters.hpp : 125) Processed 4630342 reads 0:00:18.791 4641M / 5716M INFO General (kmer_splitters.hpp : 125) Processed 6199397 reads 0:00:23.609 4641M / 5716M INFO General (kmer_splitters.hpp : 125) Processed 7746847 reads 0:00:28.511 4641M / 5717M INFO General (kmer_splitters.hpp : 125) Processed 9311174 reads 0:00:32.337 4641M / 5717M INFO General (kmer_splitters.hpp : 125) Processed 11155882 reads 0:00:32.893 4641M / 5717M INFO General (kmer_splitters.hpp : 125) Processed 11264410 reads 0:00:32.894 1M / 5717M INFO General (kmer_splitters.hpp : 131) Used 11264410 reads 0:00:32.902 1M / 5717M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:00:42.291 1M / 5717M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 641811314 kmers in total. 0:00:42.291 1M / 5717M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:00:42.305 1M / 5717M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:00:42.305 1M / 5717M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:00:42.306 1M / 5717M INFO General (file_limit.hpp : 32) Open file limit set to 500000 0:00:42.306 1M / 5717M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:00:42.306 1M / 5717M INFO General (kmer_splitter.hpp : 101) Using cell size of 209715 0:00:43.252 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 5786091 kmers 0:00:43.913 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 11883992 kmers 0:00:44.568 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 17994834 kmers 0:00:45.307 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 24678510 kmers 0:00:46.100 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 31320284 kmers 0:00:46.886 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 37869204 kmers 0:00:47.683 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 44528996 kmers 0:00:48.466 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 50783812 kmers 0:00:49.295 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 56779403 kmers 0:00:50.079 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 62798292 kmers 0:00:50.876 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 69872974 kmers 0:00:51.639 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 75979008 kmers 0:00:52.352 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 82065817 kmers 0:00:53.145 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 88757298 kmers 0:00:53.885 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 95380699 kmers 0:00:54.646 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 101925624 kmers 0:00:55.425 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 108592043 kmers 0:00:59.253 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 140154557 kmers 0:01:14.497 4641M / 5717M INFO General (kmer_splitters.hpp : 194) Processed 268543093 kmers 0:01:46.938 4641M / 6211M INFO General (kmer_splitters.hpp : 194) Processed 538022592 kmers 0:01:59.382 4641M / 6683M INFO General (kmer_splitters.hpp : 199) Used 641815714 kmers. 0:01:59.382 1M / 6683M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:02:18.273 1M / 8868M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 642954780 kmers in total. 0:02:18.273 1M / 8868M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:02:32.264 464M / 8868M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 642954780 kmers, 464440968 bytes occupied (5.77883 bits per kmer). 0:02:32.264 464M / 8868M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:03:06.902 1080M / 8868M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:04:36.364 1080M / 8868M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:04:36.633 1080M / 8868M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 0:04:36.633 1080M / 8868M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 0:04:54.639 1083M / 8868M INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 29912 0:04:54.639 1080M / 8868M INFO Early A/T remover (early_simplification.hpp : 179) 29848 128-mers were removed by early poly A/T remover 0:04:54.743 1080M / 8868M INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 0:06:09.548 1082M / 8868M INFO Early A/T remover (early_simplification.hpp : 330) Clipped tips: 16131 0:06:09.548 1080M / 8868M INFO Early A/T remover (early_simplification.hpp : 265) 1531176 128-mers were removed by early poly A/T tip clipper 0:06:09.819 1080M / 8868M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:06:09.822 1080M / 8868M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:07:59.021 1665M / 8868M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 7042920 sequences extracted 0:08:48.644 1665M / 8868M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:08:57.460 1666M / 8868M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 14 loops collected 0:08:57.760 1665M / 8868M INFO General (debruijn_graph_constructor: 487) Total 14085868 edges to create 0:08:57.760 2211M / 8868M INFO General (debruijn_graph_constructor: 489) Collecting link records 0:09:01.389 2428M / 8868M INFO General (debruijn_graph_constructor: 491) Ordering link records 0:09:01.547 2428M / 8868M INFO General (debruijn_graph_constructor: 493) Sorting done 0:09:01.612 2492M / 8868M INFO General (debruijn_graph_constructor: 503) Total 8195295 vertices to create 0:09:01.613 3250M / 8868M INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:09:08.079 2864M / 8868M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:09:08.079 2864M / 8868M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:09:22.377 3325M / 8868M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 641811314 kmers, 463615152 bytes occupied (5.77883 bits per kmer). 0:09:22.734 5777M / 8868M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:10:11.216 5777M / 8868M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:10:56.795 5777M / 8868M INFO General (coverage_filling.hpp : 82) Processed 8000000 edges 0:11:31.389 5777M / 8868M INFO General (coverage_filling.hpp : 82) Processed 14074801 edges 0:11:41.473 1785M / 8868M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:11:42.942 1785M / 8868M INFO ThresholdFinder (ec_threshold_finder.hpp : 117) Bucket size: 5 0:11:42.946 1785M / 8868M INFO General (genomic_info_filler.cpp : 39) Average edge coverage: 1.31273 0:11:42.946 1785M / 8868M INFO General (genomic_info_filler.cpp : 40) Graph threshold: 91 0:11:42.946 1785M / 8868M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 1.31273 0:11:42.946 1785M / 8868M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:11:42.946 1785M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 0:11:42.955 1794M / 8868M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:11:44.509 2066M / 8868M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 7469670 out of 14074801, length: 981891668 0:11:45.154 2138M / 8868M INFO General (edge_index.hpp : 167) Using small index (max_id = 14156300) 0:11:48.229 2138M / 8868M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:13:12.080 2513M / 8868M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 535681180 kmers, 386904096 bytes occupied (5.77812 bits per kmer). 0:13:12.564 6601M / 8868M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:13:47.678 6617M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:13:47.716 6663M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:13:47.860 6679M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:13:47.951 6695M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:13:54.834 6706M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1443408 reads 0:14:00.758 6717M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1754308 reads 0:14:07.126 6648M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 2154308 reads 0:14:16.550 6748M / 8868M INFO General (sequence_mapper_notifier.h: 95) Total 2487008 reads processed 0:14:19.011 2153M / 8868M INFO General (gap_closer.cpp : 452) Initializing gap closer 0:14:19.083 2153M / 8868M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:14:30.996 2153M / 8868M INFO GapCloser (gap_closer.cpp : 393) Closing short gaps complete: filled 177 gaps after checking 1157971 candidates 0:14:31.148 2153M / 8868M INFO General (gap_closer.cpp : 456) Gap closer done 0:14:31.669 1785M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:14:31.669 1785M / 8868M INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 0:14:31.669 1785M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 0:14:31.964 1785M / 8868M INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 0:14:31.965 1785M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 0:14:33.114 1781M / 8868M INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 87046 times 0:14:33.119 1781M / 8868M INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 0:14:40.885 1763M / 8868M INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 5/54/5 0:14:40.891 1763M / 8868M INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 172/791/234933 0:14:40.891 1760M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:14:40.891 1760M / 8868M INFO General (simplification.cpp : 368) Graph simplification started 0:14:40.891 1760M / 8868M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:14:40.891 1760M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:14:40.891 1760M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:14:40.891 1760M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:14:45.017 1709M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 633834 times 0:14:45.046 1709M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:14:46.035 1699M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 216873 times 0:14:46.040 1699M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:28.736 3762M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 99347 times 0:15:28.741 3762M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:29.066 3753M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 322 times 0:15:29.071 3753M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:29.358 3744M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 4495 times 0:15:29.363 3744M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:29.409 3728M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 81 times 0:15:29.414 3728M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:29.420 3728M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 15 times 0:15:29.424 3728M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:29.428 3728M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 1 times 0:15:29.432 3728M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:29.436 3728M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:29.440 3728M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:29.444 3728M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:29.448 3728M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:29.451 3728M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:29.455 3728M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:29.459 3728M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:29.463 3728M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:30.167 3780M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:38.349 3678M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 924592 times 0:15:38.382 3678M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:15:38.387 3678M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:38.711 3660M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 14346 times 0:15:38.717 3660M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:39.077 3641M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 25137 times 0:15:39.084 3641M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:39.588 3627M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 493 times 0:15:39.596 3627M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:39.610 3627M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 20 times 0:15:39.615 3627M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:39.619 3626M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 1 times 0:15:39.624 3626M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:39.628 3626M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:39.632 3626M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:39.635 3626M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:39.639 3626M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:39.643 3626M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:39.646 3626M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:39.650 3626M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:39.654 3626M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:39.815 3590M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:39.837 3590M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1951 times 0:15:39.841 3590M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:15:39.845 3590M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:40.073 3590M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 688 times 0:15:40.078 3590M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:40.315 3590M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 1716 times 0:15:40.320 3590M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:40.547 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 22 times 0:15:40.552 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:40.556 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 0:15:40.561 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:40.565 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:40.569 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:40.573 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:40.576 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:40.580 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:40.584 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:40.588 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:40.591 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:40.595 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:40.599 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:40.762 3591M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:40.768 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 152 times 0:15:40.772 3591M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:15:40.776 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:41.005 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 148 times 0:15:41.010 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:41.246 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 244 times 0:15:41.252 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:41.467 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 5 times 0:15:41.472 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:41.477 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:41.481 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:41.485 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:41.489 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:41.493 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:41.497 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:41.661 3591M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:41.666 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 35 times 0:15:41.670 3591M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:15:41.674 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:41.901 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 45 times 0:15:41.907 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:42.137 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 36 times 0:15:42.143 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:42.357 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:42.362 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:42.367 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:42.370 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:42.374 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:42.378 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:42.382 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:42.385 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:42.548 3591M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:42.554 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 17 times 0:15:42.558 3591M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:15:42.562 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:42.792 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 17 times 0:15:42.798 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:43.035 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 7 times 0:15:43.041 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:43.253 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:43.258 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:43.262 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:43.267 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:43.271 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:43.274 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:43.278 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:43.282 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:43.444 3591M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:43.450 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 13 times 0:15:43.454 3591M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:15:43.458 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:43.681 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 10 times 0:15:43.687 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:43.916 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 2 times 0:15:43.922 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:44.135 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:44.140 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:44.144 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:44.148 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:44.153 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:44.156 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:44.160 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:44.164 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:44.327 3591M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:44.332 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 9 times 0:15:44.336 3591M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:15:44.340 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:44.570 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 4 times 0:15:44.576 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:44.805 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:44.811 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:45.026 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:45.031 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:45.035 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:45.039 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:45.043 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:45.046 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:45.050 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:45.054 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:45.217 3591M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:45.223 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 3 times 0:15:45.227 3591M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:15:45.230 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:45.456 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:15:45.461 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:45.689 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:45.695 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:45.912 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:45.917 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:45.922 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:45.926 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:45.929 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:45.933 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:45.937 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:45.941 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:46.103 3591M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:46.109 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 2 times 0:15:46.113 3591M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:15:46.117 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:46.346 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:15:46.352 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:46.583 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:46.589 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:46.801 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:46.806 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:46.810 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:46.814 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:46.819 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:46.822 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:46.826 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:46.830 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:46.993 3591M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:46.999 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 1 times 0:15:47.003 3591M / 8868M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:15:47.006 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:15:47.236 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:15:47.241 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:15:47.472 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:15:47.477 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:15:47.691 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:15:47.696 3591M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:15:47.860 3591M / 8868M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:15:47.865 3591M / 8868M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:15:47.981 3584M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 0:15:47.994 3593M / 8868M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:15:49.319 3737M / 8868M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 4968626 out of 5044332, length: 795588268 0:15:49.809 3777M / 8868M INFO General (edge_index.hpp : 167) Using small index (max_id = 14156300) 0:15:51.965 3777M / 8868M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:16:52.530 4057M / 8868M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 399663141 kmers, 288687976 bytes occupied (5.77863 bits per kmer). 0:16:52.903 7110M / 8868M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:17:31.508 7127M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:17:31.969 7150M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:17:32.951 7178M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:17:34.101 7216M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:17:57.131 7227M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1443408 reads 0:18:03.268 7189M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1643408 reads 0:18:08.261 7195M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 2154308 reads 0:18:33.995 7302M / 8868M INFO General (sequence_mapper_notifier.h: 95) Total 2487008 reads processed 0:18:36.489 3969M / 8868M INFO General (gap_closer.cpp : 452) Initializing gap closer 0:18:36.579 3969M / 8868M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:18:40.581 3969M / 8868M INFO GapCloser (gap_closer.cpp : 393) Closing short gaps complete: filled 465 gaps after checking 490965 candidates 0:18:40.699 3969M / 8868M INFO General (gap_closer.cpp : 456) Gap closer done 0:18:41.144 3584M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 0:18:41.174 3584M / 8868M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 0:18:41.178 3584M / 8868M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 0:18:41.181 3584M / 8868M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 0:18:41.185 3584M / 8868M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:18:41.189 3584M / 8868M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:18:41.193 3584M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:18:41.534 3584M / 8868M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 6 times 0:18:41.541 3584M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:18:41.760 3584M / 8868M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 4684 times 0:18:41.766 3584M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:18:50.381 3584M / 8868M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 1 times 0:18:50.386 3584M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:18:50.608 3584M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 68 times 0:18:50.613 3584M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:18:51.006 3583M / 8868M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 33191 times 0:18:51.014 3583M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:18:51.263 3584M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 104 times 0:18:51.268 3584M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:18:51.457 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:18:51.462 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:18:51.964 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 452 times 0:18:51.969 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:18:52.312 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 15 times 0:18:52.317 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:18:52.503 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 36 times 0:18:52.508 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:19:01.046 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 1 times 0:19:01.051 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:19:01.264 3584M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 26 times 0:19:01.270 3584M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:19:01.484 3584M / 8868M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 131 times 0:19:01.490 3584M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:19:01.686 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 1 times 0:19:01.691 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:19:01.883 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:19:01.888 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:19:02.391 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:19:02.396 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:19:02.400 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 0:19:02.404 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:19:02.591 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 0:19:02.597 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:19:11.029 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 0:19:11.034 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:19:11.039 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:19:11.043 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:19:11.047 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 0:19:11.052 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:19:11.056 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:19:11.060 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:19:11.064 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:19:11.067 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:19:11.071 3585M / 8868M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:19:11.075 3585M / 8868M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 0:19:12.564 3585M / 8868M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 0:19:15.859 3419M / 8868M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 2248019 times 0:19:15.880 3386M / 8868M INFO General (simplification.cpp : 491) Counting average coverage 0:19:15.992 3386M / 8868M INFO General (simplification.cpp : 497) Average coverage = 3.62753 0:19:15.997 3386M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Mismatch Correction (id: mismatch_correction) 0:19:16.000 3386M / 8868M INFO General (graph_pack.cpp : 67) Index refill 0:19:16.004 3386M / 8868M INFO General (edge_index.hpp : 156) Using small index (max_id = 14156300) 0:19:16.196 3386M / 8868M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:19:18.494 3409M / 8868M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 33457346 kmers, 24259546 bytes occupied (5.80071 bits per kmer). 0:19:18.529 3666M / 8868M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 0:19:19.908 3666M / 8868M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 25809626 kmers to process 0:19:27.540 3666M / 8868M INFO General (graph_pack.cpp : 79) Normalizing done 0:19:27.544 3666M / 8868M INFO General (mismatch_correction.cpp : 400) Collect potential mismatches 0:19:32.184 3675M / 8868M INFO General (mismatch_correction.cpp : 193) Total 71870 edges (out of 415114) with 1082420 potential mismatch positions (15.0608 positions per edge) 0:19:32.194 3675M / 8868M INFO General (mismatch_correction.cpp : 402) Potential mismatches collected 0:19:47.580 3676M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:19:52.022 3681M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:19:53.141 3686M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:19:55.638 3691M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:19:59.835 3691M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:19:59.941 3692M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:20:13.355 3701M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:20:42.925 3717M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 4200000 reads 0:21:58.096 3722M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 8530800 reads 0:22:38.358 3847M / 8868M INFO General (sequence_mapper_notifier.h: 95) Total 9948032 reads processed 0:22:38.641 3749M / 8868M INFO General (mismatch_correction.cpp : 395) All edges processed 0:22:38.664 3666M / 8868M INFO General (mismatch_correction.cpp : 450) Corrected 28 nucleotides 0:22:38.671 3666M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:22:38.675 3666M / 8868M INFO General (contig_output.hpp : 16) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/before_rr.fasta 0:22:39.646 3666M / 8868M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/assembly_graph_after_simplification.gfa 0:22:40.205 3666M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Paired Information Counting (id: late_pair_info_count) 0:22:40.795 3743M / 8868M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 25815306 kmers to process 0:22:48.466 3743M / 8868M INFO General (graph_pack.cpp : 79) Normalizing done 0:22:48.507 3743M / 8868M INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 500 0:22:48.512 3743M / 8868M INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 0:22:48.516 3743M / 8868M INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 0:22:48.530 3887M / 8868M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 0:23:33.167 3887M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:23:43.889 3887M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:23:44.230 3887M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:23:50.383 3887M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:23:57.332 3887M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:23:57.567 3887M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:24:45.510 3887M / 8868M INFO General (sequence_mapper_notifier.h: 95) Total 2487008 reads processed 0:24:45.751 3887M / 8868M INFO General (pair_info_count.cpp : 220) Edge pairs: 781441 0:24:45.756 3887M / 8868M INFO General (pair_info_count.cpp : 224) 1432 paired reads (0.0575792% of all) aligned to long edges 0:24:45.760 3743M / 8868M INFO General (pair_info_count.cpp : 373) Insert size = 429.85, deviation = 163.261, left quantile = 266, right quantile = 645, read length = 300 0:24:45.764 3743M / 8868M INFO General (pair_info_count.cpp : 402) Mapping library #0 0:24:45.768 3743M / 8868M INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 0:24:45.772 3743M / 8868M INFO General (pair_info_count.cpp : 302) Left insert size quantile 266, right insert size quantile 645, filtering threshold 0, rounding threshold 0 0:24:45.784 3752M / 8868M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 0:25:30.971 3775M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:25:41.008 3783M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:25:41.342 3791M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:25:47.565 3797M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:25:54.472 3798M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:25:54.696 3799M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:26:42.084 3822M / 8868M INFO General (sequence_mapper_notifier.h: 95) Total 2487008 reads processed 0:26:42.130 3813M / 8868M INFO General (pair_info_count.cpp : 411) Mapping single reads of library #0 0:26:42.141 3813M / 8868M INFO General (pair_info_count.cpp : 266) Will calculate lib coverage as well 0:26:42.146 3813M / 8868M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 0:27:03.198 3813M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 200000 reads 0:27:08.775 3815M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 400000 reads 0:27:08.943 3816M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 600000 reads 0:27:12.177 3818M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 800000 reads 0:27:16.550 3819M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1000000 reads 0:27:16.761 3820M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 1200000 reads 0:27:37.738 3821M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 2200000 reads 0:28:25.477 3822M / 8868M INFO General (sequence_mapper_notifier.h: 77) Processed 4287200 reads 0:28:38.526 3833M / 8868M INFO General (sequence_mapper_notifier.h: 95) Total 4974016 reads processed 0:28:38.545 3830M / 8868M INFO General (pair_info_count.cpp : 413) Total paths obtained from single reads: 0 0:28:38.550 3830M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Distance Estimation (id: distance_estimation) 0:28:38.554 3830M / 8868M INFO General (distance_estimation.cpp : 179) Processing library #0 0:28:38.558 3830M / 8868M INFO General (distance_estimation.cpp : 150) Weight Filter Done 0:28:38.562 3830M / 8868M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:28:39.024 3844M / 8868M INFO General (distance_estimation.cpp : 37) Filtering info 0:28:39.033 3844M / 8868M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 906250 0:28:39.419 3825M / 8868M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 241756 0:28:39.431 3809M / 8868M INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:28:39.496 3809M / 8868M INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:28:39.501 3809M / 8868M INFO General (distance_estimation.cpp : 160) Improving paired information 0:28:40.252 3813M / 8868M INFO PairInfoImprover (pair_info_improver.hpp : 105) Paired info stats: missing = 46991; contradictional = 0 0:28:41.049 3813M / 8868M INFO PairInfoImprover (pair_info_improver.hpp : 105) Paired info stats: missing = 5358; contradictional = 0 0:28:41.058 3813M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Repeat Resolving (id: repeat_resolving) 0:28:41.063 3813M / 8868M INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 0:28:41.067 3813M / 8868M INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 0:28:41.635 4645M / 8868M INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 0:28:41.641 4645M / 8868M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 346202 0:28:41.651 4705M / 8868M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 346202 0:28:41.737 4757M / 8868M INFO General (extenders_logic.cpp : 543) Using 1 paired-end library 0:28:41.744 4757M / 8868M INFO General (extenders_logic.cpp : 544) Using 1 paired-end scaffolding library 0:28:41.750 4757M / 8868M INFO General (extenders_logic.cpp : 545) Using 0 single read libraries 0:28:41.756 4757M / 8868M INFO General (launcher.cpp : 447) Total number of extenders is 5 0:28:41.761 4757M / 8868M INFO General (path_extenders.cpp : 36) Processed 0 paths from 206800 (0%) 0:28:41.776 4758M / 8868M INFO General (path_extenders.cpp : 34) Processed 128 paths from 206800 (0%) 0:28:41.793 4759M / 8868M INFO General (path_extenders.cpp : 34) Processed 256 paths from 206800 (0%) 0:28:41.811 4760M / 8868M INFO General (path_extenders.cpp : 34) Processed 512 paths from 206800 (0%) 0:28:41.847 4763M / 8868M INFO General (path_extenders.cpp : 34) Processed 1024 paths from 206800 (0%) 0:28:41.907 4769M / 8868M INFO General (path_extenders.cpp : 34) Processed 2048 paths from 206800 (0%) 0:28:42.040 4779M / 8868M INFO General (path_extenders.cpp : 34) Processed 4096 paths from 206800 (1%) 0:28:42.268 4800M / 8868M INFO General (path_extenders.cpp : 34) Processed 8192 paths from 206800 (3%) 0:28:42.716 4839M / 8868M INFO General (path_extenders.cpp : 34) Processed 16384 paths from 206800 (7%) 0:28:43.065 4862M / 8868M INFO General (path_extenders.cpp : 36) Processed 20681 paths from 206800 (10%) 0:28:43.602 4917M / 8868M INFO General (path_extenders.cpp : 34) Processed 32768 paths from 206800 (15%) 0:28:44.032 4956M / 8868M INFO General (path_extenders.cpp : 36) Processed 41362 paths from 206800 (20%) 0:28:44.778 5044M / 8868M INFO General (path_extenders.cpp : 36) Processed 62043 paths from 206800 (30%) 0:28:44.803 5058M / 8868M INFO General (path_extenders.cpp : 34) Processed 65536 paths from 206800 (31%) 0:28:44.901 5127M / 8868M INFO General (path_extenders.cpp : 36) Processed 82724 paths from 206800 (40%) 0:28:45.074 5208M / 8868M INFO General (path_extenders.cpp : 36) Processed 103405 paths from 206800 (50%) 0:28:45.229 5290M / 8868M INFO General (path_extenders.cpp : 36) Processed 124086 paths from 206800 (60%) 0:28:45.269 5317M / 8868M INFO General (path_extenders.cpp : 34) Processed 131072 paths from 206800 (63%) 0:28:45.830 5379M / 8868M INFO General (path_extenders.cpp : 36) Processed 144767 paths from 206800 (70%) 0:28:46.776 5445M / 8868M INFO General (path_extenders.cpp : 36) Processed 165448 paths from 206800 (80%) 0:28:46.962 5520M / 8868M INFO General (path_extenders.cpp : 36) Processed 186129 paths from 206800 (90%) 0:28:47.155 5593M / 8868M INFO General (launcher.cpp : 250) Finalizing paths 0:28:47.161 5593M / 8868M INFO General (launcher.cpp : 252) Deduplicating paths 0:28:47.286 5583M / 8868M INFO General (launcher.cpp : 256) Paths deduplicated 0:28:47.292 5583M / 8868M INFO General (launcher.cpp : 263) Overlaps will not be removed 0:28:47.599 5609M / 8868M INFO General (launcher.cpp : 273) Paths finalized 0:28:47.605 5609M / 8868M INFO General (launcher.cpp : 454) Closing gaps in paths 0:28:48.089 6388M / 8868M INFO General (launcher.cpp : 484) Gap closing completed 0:28:48.203 6417M / 8868M INFO General (launcher.cpp : 302) Traversing tandem repeats 0:28:49.141 6417M / 8868M INFO General (launcher.cpp : 312) Traversed 0 loops 0:28:49.148 6417M / 8868M INFO General (launcher.cpp : 250) Finalizing paths 0:28:49.154 6417M / 8868M INFO General (launcher.cpp : 252) Deduplicating paths 0:28:49.304 6409M / 8868M INFO General (launcher.cpp : 256) Paths deduplicated 0:28:49.311 6409M / 8868M INFO General (launcher.cpp : 263) Overlaps will not be removed 0:28:49.588 6432M / 8868M INFO General (launcher.cpp : 273) Paths finalized 0:28:49.595 6432M / 8868M INFO General (launcher.cpp : 499) Finalizing paths - hard 0:28:49.778 7228M / 8868M INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 323 0:28:49.785 7228M / 8868M INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 323 0:28:49.792 7228M / 8868M INFO General (launcher.cpp : 297) Length cutoff: 323 0:28:49.885 6500M / 8868M INFO General (launcher.cpp : 295) Read length relative cutoff 2 converted to 473 0:28:49.892 6500M / 8868M INFO General (launcher.cpp : 296) Read length absolute cutoff 180 bp converted to 473 0:28:49.898 6500M / 8868M INFO General (launcher.cpp : 297) Length cutoff: 473 0:28:49.911 6474M / 8868M INFO General (launcher.cpp : 295) Read length relative cutoff 2 converted to 473 0:28:49.917 6474M / 8868M INFO General (launcher.cpp : 296) Read length absolute cutoff 180 bp converted to 473 0:28:49.924 6474M / 8868M INFO General (launcher.cpp : 297) Length cutoff: 473 0:28:50.021 6434M / 8868M INFO General (launcher.cpp : 499) Finalizing paths - soft 0:28:50.197 7229M / 8868M INFO General (launcher.cpp : 295) Read length relative cutoff 1.05 converted to 188 0:28:50.203 7229M / 8868M INFO General (launcher.cpp : 296) Read length absolute cutoff 85 bp converted to 188 0:28:50.210 7229M / 8868M INFO General (launcher.cpp : 297) Length cutoff: 188 0:28:50.291 6613M / 8868M INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 323 0:28:50.298 6613M / 8868M INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 323 0:28:50.304 6613M / 8868M INFO General (launcher.cpp : 297) Length cutoff: 323 0:28:50.318 6592M / 8868M INFO General (launcher.cpp : 295) Read length relative cutoff 1.2 converted to 233 0:28:50.325 6592M / 8868M INFO General (launcher.cpp : 296) Read length absolute cutoff 100 bp converted to 233 0:28:50.331 6592M / 8868M INFO General (launcher.cpp : 297) Length cutoff: 233 0:28:50.624 6439M / 8868M INFO General (launcher.cpp : 507) Finalizing main paths 0:28:50.632 6439M / 8868M INFO General (launcher.cpp : 295) Read length relative cutoff 1.3 converted to 263 0:28:50.638 6439M / 8868M INFO General (launcher.cpp : 296) Read length absolute cutoff 110 bp converted to 263 0:28:50.644 6439M / 8868M INFO General (launcher.cpp : 297) Length cutoff: 263 0:28:50.743 5737M / 8868M INFO General (launcher.cpp : 295) Read length relative cutoff 1.6 converted to 353 0:28:50.750 5737M / 8868M INFO General (launcher.cpp : 296) Read length absolute cutoff 140 bp converted to 353 0:28:50.755 5737M / 8868M INFO General (launcher.cpp : 297) Length cutoff: 353 0:28:50.769 5716M / 8868M INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 323 0:28:50.777 5716M / 8868M INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 323 0:28:50.783 5716M / 8868M INFO General (launcher.cpp : 297) Length cutoff: 323 0:28:50.797 5709M / 8868M INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 0:28:51.123 3879M / 8868M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:28:51.153 3879M / 8868M INFO General (contig_output.hpp : 16) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/before_rr.fasta 0:28:52.129 3879M / 8868M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/assembly_graph_with_scaffolds.gfa 0:28:52.676 3879M / 8868M INFO General (contig_output_stage.cpp : 165) Outputting FastG graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/assembly_graph.fastg 0:28:54.430 3898M / 8868M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/transcripts.fasta 0:28:54.488 3898M / 8868M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/transcripts.paths 0:28:54.537 3898M / 8868M INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 0:28:54.572 3879M / 8868M INFO General (pipeline.cpp : 287) SPAdes finished 0:28:57.307 1M / 8868M INFO General (main.cpp : 136) Assembling time: 0 hours 28 minutes 57 seconds ===== K127 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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/before_rr.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/before_rr.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/assembly_graph_after_simplification.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/assembly_graph_after_simplification.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/transcripts.paths /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/transcripts.paths /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/assembly_graph_with_scaffolds.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/assembly_graph_with_scaffolds.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/assembly_graph.fastg /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/assembly_graph.fastg /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/hard_filtered_final_paths.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/hard_filtered_transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/K127/soft_filtered_final_paths.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/scaffolds.fasta --misc_dir /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/transcripts.paths * Hard filtered transcripts are in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/hard_filtered_transcripts.fasta * Soft filtered transcripts are in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/soft_filtered_transcripts.fasta * Assembly graph is in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/nmdc_metat/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/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/d37d4f1b-6cff-456a-86a3-145f2ab377ca/call-asse/metatranscriptome_assy/48eeafd8-304a-4214-88b2-0fe4f887f801/call-assy/execution/out.spades/spades.log Thank you for using SPAdes!