Command line: /SPAdes-3.15.2-Linux/bin/rnaspades.py -t 8 -m 120 -o /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades --12 /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/reads.input.fastq.gz System information: SPAdes version: 3.15.2 Python version: 3.9.16 OS: Linux-5.14.21-150400.24.81_12.0.87-cray_shasta_c-x86_64-with-glibc2.34 Output dir: /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/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/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/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/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/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/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/spades.log /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/reads.input.fastq.gz: max reads length: 150 Reads length: 150 K values to be used: [49, 73] ===== Before start started. ===== Preprocess reads started. ===== Preprocess reads finished. ===== Assembling started. ===== K49 started. == Running: /SPAdes-3.15.2-Linux/bin/spades-core /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K49/configs/config.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K49/configs/mda_mode.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K49/configs/rna_mode.info 0:00:00.000 1M / 14M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K49/configs/config.info 0:00:00.010 1M / 14M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K49/configs/mda_mode.info 0:00:00.010 1M / 14M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K49/configs/rna_mode.info 0:00:00.010 1M / 14M INFO General (memory_limit.cpp : 48) Memory limit set to 120 Gb 0:00:00.010 1M / 14M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.2, git revision aab988a9b4986906b38396da7233bb1ee02982f2 0:00:00.010 1M / 14M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.010 1M / 14M INFO General (main.cpp : 109) Assembling dataset (/pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/dataset.info) with K=49 0:00:00.010 1M / 14M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 8 0:00:00.010 1M / 14M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.010 1M / 14M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.010 1M / 14M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.010 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.010 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.010 1M / 14M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:00.010 1M / 14M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.011 1M / 14M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.011 1M / 14M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.042 14M / 17M INFO General (binary_converter.cpp : 111) 4984 reads written 0:00:00.042 7M / 17M INFO General (read_converter.cpp : 81) Converting single reads 0:00:00.043 11M / 17M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:00.043 7M / 17M INFO General (read_converter.cpp : 87) Converting merged reads 0:00:00.044 11M / 17M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:00.046 1M / 18M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:00:00.049 1M / 18M INFO General (construction.cpp : 153) Max read length 150 0:00:00.049 1M / 18M INFO General (construction.cpp : 159) Average read length 149.944 0:00:00.049 1M / 18M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:00:00.052 1M / 18M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:00:00.052 1M / 18M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:00:00.052 1M / 18M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:00:00.052 1M / 18M INFO General (kmer_splitter.hpp : 101) Using cell size of 419430 0:00:00.350 1M / 1326M INFO General (kmer_splitters.hpp : 131) Used 19936 reads 0:00:00.352 1M / 1326M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:00:00.427 1M / 1326M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 832226 kmers in total. 0:00:00.427 1M / 1326M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:00:00.441 1M / 1326M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:00:00.441 1M / 1326M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:00:00.441 1M / 1326M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:00:00.441 1M / 1326M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:00:00.441 1M / 1326M INFO General (kmer_splitter.hpp : 101) Using cell size of 419430 0:00:00.741 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 832226 kmers 0:00:00.741 4641M / 4641M INFO General (kmer_splitters.hpp : 199) Used 832226 kmers. 0:00:00.742 1M / 1361M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:00:00.819 1M / 1361M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 839733 kmers in total. 0:00:00.819 1M / 1361M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:00.849 2M / 1361M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 839733 kmers, 668096 bytes occupied (6.36484 bits per kmer). 0:00:00.849 2M / 1361M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:00:00.907 3M / 1361M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:00:00.965 3M / 1361M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:00:00.967 3M / 1361M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 0:00:00.967 3M / 1361M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 0:00:00.985 3M / 1361M INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 0 0:00:00.985 3M / 1361M INFO Early A/T remover (early_simplification.hpp : 179) 0 50-mers were removed by early poly A/T remover 0:00:00.986 3M / 1361M INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 0:00:01.023 3M / 1361M INFO Early A/T remover (early_simplification.hpp : 330) Clipped tips: 2 0:00:01.023 3M / 1361M INFO Early A/T remover (early_simplification.hpp : 265) 10 50-mers were removed by early poly A/T tip clipper 0:00:01.025 3M / 1361M INFO General (stage.cpp : 117) PROCEDURE == Early tip clipping (id: construction:early_tip_clipper) 0:00:01.025 3M / 1361M INFO General (construction.cpp : 301) Early tip clipper length bound set as (RL - K) 0:00:01.025 3M / 1361M INFO Early tip clipping (early_simplification.hpp : 47) Early tip clipping 0:00:01.042 3M / 1361M INFO Early tip clipping (early_simplification.hpp : 82) #tipped junctions: 345 0:00:01.042 3M / 1361M INFO Early tip clipping (early_simplification.hpp : 93) Clipped tips: 346 0:00:01.043 3M / 1361M INFO Early tip clipping (early_simplification.hpp : 49) 10571 50-mers were removed by early tip clipper 0:00:01.043 3M / 1361M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:00:01.045 3M / 1361M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:01.085 3M / 1361M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 8140 sequences extracted 0:00:01.118 3M / 1361M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:01.126 3M / 1361M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected 0:00:01.128 3M / 1361M INFO General (debruijn_graph_constructor: 487) Total 16282 edges to create 0:00:01.128 4M / 1361M INFO General (debruijn_graph_constructor: 489) Collecting link records 0:00:01.132 4M / 1361M INFO General (debruijn_graph_constructor: 491) Ordering link records 0:00:01.133 4M / 1361M INFO General (debruijn_graph_constructor: 493) Sorting done 0:00:01.133 4M / 1361M INFO General (debruijn_graph_constructor: 503) Total 15648 vertices to create 0:00:01.133 6M / 1361M INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:00:01.144 5M / 1361M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:00:01.144 5M / 1361M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:01.168 6M / 1361M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 832226 kmers, 662360 bytes occupied (6.36712 bits per kmer). 0:00:01.169 9M / 1361M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:00:01.197 9M / 1361M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:00:01.215 9M / 1361M INFO General (coverage_filling.hpp : 82) Processed 16282 edges 0:00:01.251 3M / 1361M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:00:01.252 3M / 1361M INFO ThresholdFinder (ec_threshold_finder.hpp : 117) Bucket size: 5 0:00:01.252 3M / 1361M INFO ThresholdFinder (ec_threshold_finder.hpp : 132) Proper threshold was not found. Threshold set to 0.1 of average coverage 0:00:01.252 3M / 1361M INFO General (genomic_info_filler.cpp : 39) Average edge coverage: 1.20852 0:00:01.252 3M / 1361M INFO General (genomic_info_filler.cpp : 40) Graph threshold: 0.120852 0:00:01.252 3M / 1361M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 0.120852 0:00:01.252 3M / 1361M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:00:01.252 3M / 1361M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:00:01.252 3M / 1361M INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 0:00:01.252 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 0:00:01.252 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 0:00:01.252 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 0:00:01.253 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 10 times 0:00:01.253 3M / 1361M INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 0:00:01.256 3M / 1361M INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 0/1/0 0:00:01.256 3M / 1361M INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 0/0/0 0:00:01.256 3M / 1361M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:00:01.256 3M / 1361M INFO General (simplification.cpp : 368) Graph simplification started 0:00:01.256 3M / 1361M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:00:01.256 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.256 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:00:01.256 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.257 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 107 times 0:00:01.257 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.257 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 107 times 0:00:01.257 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 95 times 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.259 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.259 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 1 times 0:00:01.259 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.260 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.260 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.260 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.261 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.261 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.261 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.261 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.261 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:00:01.261 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.261 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.261 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.261 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.261 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.261 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.261 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.262 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.262 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.262 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:00:01.262 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.262 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.262 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.262 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.262 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.262 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.262 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.262 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.262 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.262 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:00:01.262 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.263 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.263 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.263 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.264 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.264 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.264 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.264 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:00:01.264 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.265 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.265 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.265 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.265 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.265 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.265 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.265 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.265 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.265 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:00:01.265 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.265 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.265 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.266 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.266 3M / 1361M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.266 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.267 3M / 1361M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.267 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.267 3M / 1361M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 0:00:01.267 3M / 1361M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 0:00:01.267 3M / 1361M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 0:00:01.267 3M / 1361M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 0:00:01.267 3M / 1361M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:00:01.267 3M / 1361M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:00:01.267 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:00:01.267 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 0:00:01.267 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:00:01.267 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 0:00:01.267 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:00:01.297 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 0:00:01.297 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.298 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.298 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:00:01.298 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 3 times 0:00:01.298 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.298 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.298 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:00:01.298 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:00:01.298 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:00:01.299 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:00:01.299 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:00:01.299 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 0:00:01.299 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:00:01.299 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 0:00:01.299 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:00:01.327 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 0:00:01.327 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.328 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.328 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:00:01.328 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 0:00:01.328 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.328 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.328 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:00:01.328 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:00:01.328 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:00:01.329 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:00:01.329 3M / 1361M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 0:00:01.330 3M / 1361M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 0:00:01.335 3M / 1361M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 7073 times 0:00:01.335 3M / 1361M INFO General (simplification.cpp : 491) Counting average coverage 0:00:01.335 3M / 1361M INFO General (simplification.cpp : 497) Average coverage = 1.95245 0:00:01.335 3M / 1361M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:00:01.336 3M / 1361M INFO General (read_converter.cpp : 102) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K49/simplified_contigs 0:00:01.338 5M / 1361M INFO General (binary_converter.cpp : 111) 532 reads written 0:00:01.340 3M / 1361M INFO General (pipeline.cpp : 287) SPAdes finished 0:00:01.340 1M / 1361M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 1 seconds ===== K49 finished. ===== K73 started. == Running: /SPAdes-3.15.2-Linux/bin/spades-core /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/configs/config.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/configs/mda_mode.info /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/configs/rna_mode.info 0:00:00.000 1M / 14M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/configs/config.info 0:00:00.000 1M / 14M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/configs/mda_mode.info 0:00:00.000 1M / 14M INFO General (main.cpp : 99) Loaded config from /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/configs/rna_mode.info 0:00:00.000 1M / 14M INFO General (memory_limit.cpp : 48) Memory limit set to 120 Gb 0:00:00.000 1M / 14M INFO General (main.cpp : 107) Starting SPAdes, built from refs/heads/spades_3.15.2, git revision aab988a9b4986906b38396da7233bb1ee02982f2 0:00:00.000 1M / 14M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.000 1M / 14M INFO General (main.cpp : 109) Assembling dataset (/pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/dataset.info) with K=73 0:00:00.000 1M / 14M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 8 0:00:00.000 1M / 14M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.000 1M / 14M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.000 1M / 14M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.000 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.000 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.000 1M / 14M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:00.000 1M / 14M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 0:00:00.000 1M / 14M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.001 1M / 14M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.002 1M / 14M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:00:00.002 1M / 14M INFO General (construction.cpp : 118) Contigs from previous K will be used: /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K49/simplified_contigs 0:00:00.005 1M / 14M INFO General (construction.cpp : 153) Max read length 150 0:00:00.005 1M / 14M INFO General (construction.cpp : 159) Average read length 149.944 0:00:00.005 1M / 14M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:00:00.005 1M / 14M 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 / 14M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:00:00.005 1M / 14M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:00:00.005 1M / 14M INFO General (kmer_splitter.hpp : 101) Using cell size of 279620 0:00:00.309 1M / 1318M INFO General (kmer_splitters.hpp : 131) Used 21000 reads 0:00:00.311 1M / 1318M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:00:00.407 1M / 1318M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 649764 kmers in total. 0:00:00.407 1M / 1318M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:00:00.421 1M / 1318M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:00:00.421 1M / 1318M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 80 files using 8 threads. This might take a while. 0:00:00.421 1M / 1318M INFO General (file_limit.hpp : 32) Open file limit set to 600000 0:00:00.421 1M / 1318M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 4.99998 Gb 0:00:00.421 1M / 1318M INFO General (kmer_splitter.hpp : 101) Using cell size of 279620 0:00:00.712 4641M / 4641M INFO General (kmer_splitters.hpp : 194) Processed 649764 kmers 0:00:00.712 4641M / 4641M INFO General (kmer_splitters.hpp : 199) Used 649764 kmers. 0:00:00.713 1M / 1359M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:00:00.790 1M / 1359M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 657455 kmers in total. 0:00:00.790 1M / 1359M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:00.825 2M / 1359M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 657455 kmers, 536152 bytes occupied (6.52397 bits per kmer). 0:00:00.825 2M / 1359M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:00:00.891 3M / 1359M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:00:00.944 3M / 1359M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:00:00.947 2M / 1359M INFO General (stage.cpp : 117) PROCEDURE == Early A/T remover (id: construction:early_at_remover) 0:00:00.947 2M / 1359M INFO Early A/T remover (early_simplification.hpp : 176) Remove short poly A/T edges 0:00:00.962 2M / 1359M INFO Early A/T remover (early_simplification.hpp : 254) Links removed: 0 0:00:00.962 2M / 1359M INFO Early A/T remover (early_simplification.hpp : 179) 0 74-mers were removed by early poly A/T remover 0:00:00.963 2M / 1359M INFO Early A/T remover (early_simplification.hpp : 262) Remove poly A/T tips 0:00:00.993 2M / 1359M INFO Early A/T remover (early_simplification.hpp : 330) Clipped tips: 1 0:00:00.993 2M / 1359M INFO Early A/T remover (early_simplification.hpp : 265) 8 74-mers were removed by early poly A/T tip clipper 0:00:00.995 2M / 1359M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:00:00.996 2M / 1359M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:01.023 3M / 1359M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 8560 sequences extracted 0:00:01.050 3M / 1359M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:01.058 3M / 1359M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:01.060 3M / 1359M INFO General (debruijn_graph_constructor: 487) Total 17120 edges to create 0:00:01.060 4M / 1359M INFO General (debruijn_graph_constructor: 489) Collecting link records 0:00:01.065 4M / 1359M INFO General (debruijn_graph_constructor: 491) Ordering link records 0:00:01.066 4M / 1359M INFO General (debruijn_graph_constructor: 493) Sorting done 0:00:01.066 4M / 1359M INFO General (debruijn_graph_constructor: 503) Total 16251 vertices to create 0:00:01.066 6M / 1359M INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:00:01.083 5M / 1359M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:00:01.083 5M / 1359M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:01.111 6M / 1359M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 649764 kmers, 530624 bytes occupied (6.53313 bits per kmer). 0:00:01.112 8M / 1359M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:00:01.134 8M / 1359M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:00:01.152 8M / 1359M INFO General (coverage_filling.hpp : 82) Processed 17120 edges 0:00:01.194 3M / 1359M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:00:01.194 3M / 1359M INFO ThresholdFinder (ec_threshold_finder.hpp : 117) Bucket size: 5 0:00:01.194 3M / 1359M INFO ThresholdFinder (ec_threshold_finder.hpp : 132) Proper threshold was not found. Threshold set to 0.1 of average coverage 0:00:01.195 3M / 1359M INFO General (genomic_info_filler.cpp : 39) Average edge coverage: 1.18039 0:00:01.195 3M / 1359M INFO General (genomic_info_filler.cpp : 40) Graph threshold: 0.118039 0:00:01.195 3M / 1359M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 0.118039 0:00:01.195 3M / 1359M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:00:01.195 3M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 0:00:01.201 12M / 1359M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:01.205 13M / 1359M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 16380 out of 17120, length: 1267031 0:00:01.205 13M / 1359M INFO General (edge_index.hpp : 167) Using small index (max_id = 17208) 0:00:01.209 13M / 1359M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:01.253 14M / 1359M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 646263 kmers, 467520 bytes occupied (5.78737 bits per kmer). 0:00:01.253 19M / 1359M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:00:01.280 19M / 1359M INFO General (sequence_mapper_notifier.h: 95) Total 4984 reads processed 0:00:01.285 13M / 1359M INFO General (gap_closer.cpp : 452) Initializing gap closer 0:00:01.285 13M / 1359M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:00:01.292 14M / 1359M INFO GapCloser (gap_closer.cpp : 393) Closing short gaps complete: filled 81 gaps after checking 1001 candidates 0:00:01.292 14M / 1359M INFO General (gap_closer.cpp : 456) Gap closer done 0:00:01.293 4M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Raw Simplification (id: raw_simplification) 0:00:01.293 4M / 1359M INFO General (simplification.cpp : 106) PROCEDURE == Initial cleaning 0:00:01.293 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T short edge remover 0:00:01.293 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) poly A/T short edge remover triggered 0 times 0:00:01.293 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running poly A/T tip clipper 0:00:01.294 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) poly A/T tip clipper triggered 20 times 0:00:01.294 4M / 1359M INFO General (graph_simplification.hpp : 703) Removing loops and rc loops with erroneous connections 0:00:01.297 4M / 1359M INFO ECLoopRemover (erroneous_connection_remov: 406) Loops: accurately removed/deadend removed/other: 0/0/0 0:00:01.297 4M / 1359M INFO ECLoopRemover (erroneous_connection_remov: 407) RC loops: accurately removed/deadend removed/other: 0/0/0 0:00:01.297 4M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Simplification (id: simplification) 0:00:01.297 4M / 1359M INFO General (simplification.cpp : 368) Graph simplification started 0:00:01.297 4M / 1359M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:00:01.297 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.297 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 1 0:00:01.297 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.299 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 378 times 0:00:01.299 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.299 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 26 times 0:00:01.299 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.300 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 8 times 0:00:01.300 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.300 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.300 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.300 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.300 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.300 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.300 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.300 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.300 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.300 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 2 0:00:01.300 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 2 times 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.301 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.301 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 3 0:00:01.301 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.302 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.302 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 4 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.302 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.303 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.303 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 5 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.303 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.303 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 6 0:00:01.303 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.304 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.304 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 7 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.304 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.305 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.305 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 8 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.305 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.305 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 9 0:00:01.305 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.306 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.306 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 10 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.306 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.307 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.307 4M / 1359M INFO General (simplification.cpp : 373) PROCEDURE == Simplification cycle, iteration 11 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Dead end clipper 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Dead end clipper triggered 0 times 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Low coverage edge remover 0:00:01.307 4M / 1359M INFO ConditionParser (graph_simplification.hpp : 179) Creating relative coverage EC condition with threshold 1 0:00:01.307 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Low coverage edge remover triggered 0 times 0:00:01.308 4M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: late_gapcloser) 0:00:01.311 13M / 1359M INFO General (edge_index.hpp : 115) Size of edge index entries: 12/8 0:00:01.314 14M / 1359M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 15247 out of 15252, length: 1274320 0:00:01.314 14M / 1359M INFO General (edge_index.hpp : 167) Using small index (max_id = 34413) 0:00:01.317 14M / 1359M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:01.359 14M / 1359M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 637473 kmers, 461184 bytes occupied (5.78765 bits per kmer). 0:00:01.360 19M / 1359M INFO General (edge_index_builders.hpp : 265) Collecting edge information from graph, this takes a while. 0:00:01.386 20M / 1359M INFO General (sequence_mapper_notifier.h: 95) Total 4984 reads processed 0:00:01.390 14M / 1359M INFO General (gap_closer.cpp : 452) Initializing gap closer 0:00:01.390 14M / 1359M INFO GapCloser (gap_closer.cpp : 359) Closing short gaps 0:00:01.396 14M / 1359M INFO GapCloser (gap_closer.cpp : 393) Closing short gaps complete: filled 8 gaps after checking 926 candidates 0:00:01.396 14M / 1359M INFO General (gap_closer.cpp : 456) Gap closer done 0:00:01.397 4M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Simplification Cleanup (id: simplification_cleanup) 0:00:01.397 4M / 1359M INFO General (simplification.cpp : 176) PROCEDURE == Post simplification 0:00:01.397 4M / 1359M INFO General (graph_simplification.hpp : 448) Disconnection of relatively low covered edges disabled 0:00:01.397 4M / 1359M INFO General (graph_simplification.hpp : 485) Complex tip clipping disabled 0:00:01.397 4M / 1359M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:00:01.397 4M / 1359M INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:00:01.397 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:00:01.397 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 0:00:01.397 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:00:01.397 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 0:00:01.397 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:00:01.431 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 0:00:01.431 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.431 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.431 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:00:01.431 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 4 times 0:00:01.431 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.432 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.432 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:00:01.432 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:00:01.432 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:00:01.433 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:00:01.433 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage erroneous connection remover 0:00:01.433 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Relative coverage erroneous connection remover triggered 0 times 0:00:01.433 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Relative coverage component remover 0:00:01.433 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Relative coverage component remover triggered 0 times 0:00:01.433 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Complex bulge remover 0:00:01.467 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Complex bulge remover triggered 0 times 0:00:01.467 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Tip clipper 0:00:01.467 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Tip clipper triggered 0 times 0:00:01.467 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Final tip clipper 0:00:01.468 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Final tip clipper triggered 0 times 0:00:01.468 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Bulge remover 0:00:01.468 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Bulge remover triggered 0 times 0:00:01.468 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Final bulge remover 0:00:01.468 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Final bulge remover triggered 0 times 0:00:01.468 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running AT Tips 0:00:01.469 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) AT Tips triggered 0 times 0:00:01.469 4M / 1359M INFO General (simplification.cpp : 327) Disrupting self-conjugate edges 0:00:01.470 4M / 1359M INFO Simplification (parallel_processing.hpp : 167) Running Removing isolated edges 0:00:01.475 4M / 1359M INFO Simplification (parallel_processing.hpp : 170) Removing isolated edges triggered 7130 times 0:00:01.476 4M / 1359M INFO General (simplification.cpp : 491) Counting average coverage 0:00:01.476 4M / 1359M INFO General (simplification.cpp : 497) Average coverage = 1.6726 0:00:01.476 4M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Mismatch Correction (id: mismatch_correction) 0:00:01.476 4M / 1359M INFO General (graph_pack.cpp : 67) Index refill 0:00:01.476 4M / 1359M INFO General (edge_index.hpp : 156) Using small index (max_id = 34413) 0:00:01.476 4M / 1359M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:01.481 4M / 1359M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 80294 kmers, 58736 bytes occupied (5.85209 bits per kmer). 0:00:01.481 4M / 1359M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 0:00:01.484 4M / 1359M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 1316 kmers to process 0:00:01.484 4M / 1359M INFO General (graph_pack.cpp : 79) Normalizing done 0:00:01.484 4M / 1359M INFO General (mismatch_correction.cpp : 400) Collect potential mismatches 0:00:01.484 4M / 1359M INFO General (mismatch_correction.cpp : 193) Total 12 edges (out of 962) with 22 potential mismatch positions (1.83333 positions per edge) 0:00:01.485 4M / 1359M INFO General (mismatch_correction.cpp : 402) Potential mismatches collected 0:00:01.509 5M / 1359M INFO General (sequence_mapper_notifier.h: 95) Total 19936 reads processed 0:00:01.510 4M / 1359M INFO General (mismatch_correction.cpp : 395) All edges processed 0:00:01.510 4M / 1359M INFO General (mismatch_correction.cpp : 450) Corrected 0 nucleotides 0:00:01.510 4M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:00:01.510 4M / 1359M INFO General (contig_output.hpp : 16) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/before_rr.fasta 0:00:01.514 4M / 1359M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/assembly_graph_after_simplification.gfa 0:00:01.516 4M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Paired Information Counting (id: late_pair_info_count) 0:00:01.517 5M / 1359M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 1316 kmers to process 0:00:01.517 5M / 1359M INFO General (graph_pack.cpp : 79) Normalizing done 0:00:01.517 5M / 1359M INFO General (pair_info_count.cpp : 339) Min edge length for estimation: 500 0:00:01.517 5M / 1359M INFO General (pair_info_count.cpp : 350) Estimating insert size for library #0 0:00:01.517 5M / 1359M INFO General (pair_info_count.cpp : 202) Estimating insert size (takes a while) 0:00:01.528 149M / 1359M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 0:00:01.690 149M / 1359M INFO General (sequence_mapper_notifier.h: 95) Total 4984 reads processed 0:00:01.925 149M / 1359M INFO General (pair_info_count.cpp : 220) Edge pairs: 398 0:00:01.925 149M / 1359M INFO General (pair_info_count.cpp : 224) 21 paired reads (0.421348% of all) aligned to long edges 0:00:01.926 5M / 1359M INFO General (pair_info_count.cpp : 373) Insert size = 333.238, deviation = 60.5018, left quantile = 253, right quantile = 404, read length = 150 0:00:01.926 5M / 1359M INFO General (pair_info_count.cpp : 402) Mapping library #0 0:00:01.926 5M / 1359M INFO General (pair_info_count.cpp : 404) Mapping paired reads (takes a while) 0:00:01.926 5M / 1359M INFO General (pair_info_count.cpp : 302) Left insert size quantile 253, right insert size quantile 404, filtering threshold 0, rounding threshold 0 0:00:01.930 14M / 1359M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 0:00:01.943 14M / 1359M INFO General (sequence_mapper_notifier.h: 95) Total 4984 reads processed 0:00:01.945 5M / 1359M INFO General (pair_info_count.cpp : 411) Mapping single reads of library #0 0:00:01.952 5M / 1359M INFO General (pair_info_count.cpp : 266) Will calculate lib coverage as well 0:00:01.952 5M / 1359M INFO General (pair_info_count.cpp : 48) Selecting usual mapper 0:00:01.964 5M / 1359M INFO General (sequence_mapper_notifier.h: 95) Total 9968 reads processed 0:00:01.964 5M / 1359M INFO General (pair_info_count.cpp : 413) Total paths obtained from single reads: 0 0:00:01.964 5M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Distance Estimation (id: distance_estimation) 0:00:01.965 5M / 1359M INFO General (distance_estimation.cpp : 179) Processing library #0 0:00:01.965 5M / 1359M INFO General (distance_estimation.cpp : 150) Weight Filter Done 0:00:01.965 5M / 1359M INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:00:01.965 5M / 1359M INFO General (distance_estimation.cpp : 37) Filtering info 0:00:01.965 5M / 1359M INFO General (pair_info_filters.hpp : 242) Start filtering; library index size: 1012 0:00:01.966 5M / 1359M INFO General (pair_info_filters.hpp : 263) Done filtering; library index size: 264 0:00:01.966 5M / 1359M INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:00:01.966 5M / 1359M INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:00:01.966 5M / 1359M INFO General (distance_estimation.cpp : 160) Improving paired information 0:00:01.967 5M / 1359M INFO PairInfoImprover (pair_info_improver.hpp : 105) Paired info stats: missing = 0; contradictional = 0 0:00:01.968 5M / 1359M INFO PairInfoImprover (pair_info_improver.hpp : 105) Paired info stats: missing = 0; contradictional = 0 0:00:01.968 5M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Repeat Resolving (id: repeat_resolving) 0:00:01.968 5M / 1359M INFO General (repeat_resolving.cpp : 87) Using Path-Extend repeat resolving 0:00:01.968 5M / 1359M INFO General (launcher.cpp : 600) ExSPAnder repeat resolving tool started 0:00:01.970 7M / 1359M INFO General (launcher.cpp : 418) Creating main extenders, unique edge length = 2000 0:00:01.970 7M / 1359M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 264 0:00:01.970 7M / 1359M INFO General (extenders_logic.cpp : 345) Creating extender; library index size: 264 0:00:01.971 7M / 1359M INFO General (extenders_logic.cpp : 543) Using 1 paired-end library 0:00:01.971 7M / 1359M INFO General (extenders_logic.cpp : 544) Using 1 paired-end scaffolding library 0:00:01.971 7M / 1359M INFO General (extenders_logic.cpp : 545) Using 0 single read libraries 0:00:01.971 7M / 1359M INFO General (launcher.cpp : 447) Total number of extenders is 5 0:00:01.971 7M / 1359M INFO General (path_extenders.cpp : 36) Processed 0 paths from 480 (0%) 0:00:01.972 7M / 1359M INFO General (path_extenders.cpp : 36) Processed 49 paths from 480 (10%) 0:00:01.972 7M / 1359M INFO General (path_extenders.cpp : 36) Processed 98 paths from 480 (20%) 0:00:01.972 8M / 1359M INFO General (path_extenders.cpp : 34) Processed 128 paths from 480 (26%) 0:00:01.972 8M / 1359M INFO General (path_extenders.cpp : 36) Processed 147 paths from 480 (30%) 0:00:01.972 8M / 1359M INFO General (path_extenders.cpp : 36) Processed 196 paths from 480 (40%) 0:00:01.973 8M / 1359M INFO General (path_extenders.cpp : 36) Processed 245 paths from 480 (51%) 0:00:01.973 8M / 1359M INFO General (path_extenders.cpp : 34) Processed 256 paths from 480 (53%) 0:00:01.973 8M / 1359M INFO General (path_extenders.cpp : 36) Processed 294 paths from 480 (61%) 0:00:01.974 8M / 1359M INFO General (path_extenders.cpp : 36) Processed 343 paths from 480 (71%) 0:00:01.974 9M / 1359M INFO General (path_extenders.cpp : 36) Processed 392 paths from 480 (81%) 0:00:01.975 9M / 1359M INFO General (path_extenders.cpp : 36) Processed 441 paths from 480 (91%) 0:00:01.976 9M / 1359M INFO General (launcher.cpp : 250) Finalizing paths 0:00:01.976 9M / 1359M INFO General (launcher.cpp : 252) Deduplicating paths 0:00:01.976 9M / 1359M INFO General (launcher.cpp : 256) Paths deduplicated 0:00:01.976 9M / 1359M INFO General (launcher.cpp : 263) Overlaps will not be removed 0:00:01.977 9M / 1359M INFO General (launcher.cpp : 273) Paths finalized 0:00:01.977 9M / 1359M INFO General (launcher.cpp : 454) Closing gaps in paths 0:00:01.977 11M / 1359M INFO General (launcher.cpp : 484) Gap closing completed 0:00:01.977 11M / 1359M INFO General (launcher.cpp : 302) Traversing tandem repeats 0:00:01.979 11M / 1359M INFO General (launcher.cpp : 312) Traversed 0 loops 0:00:01.979 11M / 1359M INFO General (launcher.cpp : 250) Finalizing paths 0:00:01.979 11M / 1359M INFO General (launcher.cpp : 252) Deduplicating paths 0:00:01.979 11M / 1359M INFO General (launcher.cpp : 256) Paths deduplicated 0:00:01.979 11M / 1359M INFO General (launcher.cpp : 263) Overlaps will not be removed 0:00:01.979 11M / 1359M INFO General (launcher.cpp : 273) Paths finalized 0:00:01.979 11M / 1359M INFO General (launcher.cpp : 499) Finalizing paths - hard 0:00:01.979 13M / 1359M INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 152 0:00:01.979 13M / 1359M INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 152 0:00:01.979 13M / 1359M INFO General (launcher.cpp : 297) Length cutoff: 152 0:00:01.979 12M / 1359M INFO General (launcher.cpp : 295) Read length relative cutoff 2 converted to 227 0:00:01.979 12M / 1359M INFO General (launcher.cpp : 296) Read length absolute cutoff 180 bp converted to 227 0:00:01.979 12M / 1359M INFO General (launcher.cpp : 297) Length cutoff: 227 0:00:01.979 11M / 1359M INFO General (launcher.cpp : 295) Read length relative cutoff 2 converted to 227 0:00:01.979 11M / 1359M INFO General (launcher.cpp : 296) Read length absolute cutoff 180 bp converted to 227 0:00:01.979 11M / 1359M INFO General (launcher.cpp : 297) Length cutoff: 227 0:00:01.981 11M / 1359M INFO General (launcher.cpp : 499) Finalizing paths - soft 0:00:01.981 13M / 1359M INFO General (launcher.cpp : 295) Read length relative cutoff 1.05 converted to 84 0:00:01.981 13M / 1359M INFO General (launcher.cpp : 296) Read length absolute cutoff 85 bp converted to 84 0:00:01.981 13M / 1359M INFO General (launcher.cpp : 297) Length cutoff: 84 0:00:01.981 12M / 1359M INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 152 0:00:01.981 12M / 1359M INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 152 0:00:01.981 12M / 1359M INFO General (launcher.cpp : 297) Length cutoff: 152 0:00:01.981 12M / 1359M INFO General (launcher.cpp : 295) Read length relative cutoff 1.2 converted to 107 0:00:01.981 12M / 1359M INFO General (launcher.cpp : 296) Read length absolute cutoff 100 bp converted to 107 0:00:01.981 12M / 1359M INFO General (launcher.cpp : 297) Length cutoff: 107 0:00:01.985 11M / 1359M INFO General (launcher.cpp : 507) Finalizing main paths 0:00:01.985 11M / 1359M INFO General (launcher.cpp : 295) Read length relative cutoff 1.3 converted to 122 0:00:01.985 11M / 1359M INFO General (launcher.cpp : 296) Read length absolute cutoff 110 bp converted to 122 0:00:01.985 11M / 1359M INFO General (launcher.cpp : 297) Length cutoff: 122 0:00:01.985 11M / 1359M INFO General (launcher.cpp : 295) Read length relative cutoff 1.6 converted to 167 0:00:01.985 11M / 1359M INFO General (launcher.cpp : 296) Read length absolute cutoff 140 bp converted to 167 0:00:01.985 11M / 1359M INFO General (launcher.cpp : 297) Length cutoff: 167 0:00:01.985 10M / 1359M INFO General (launcher.cpp : 295) Read length relative cutoff 1.5 converted to 152 0:00:01.985 10M / 1359M INFO General (launcher.cpp : 296) Read length absolute cutoff 130 bp converted to 152 0:00:01.985 10M / 1359M INFO General (launcher.cpp : 297) Length cutoff: 152 0:00:01.985 10M / 1359M INFO General (launcher.cpp : 664) ExSPAnder repeat resolving tool finished 0:00:01.986 6M / 1359M INFO StageManager (stage.cpp : 185) STAGE == Contig Output (id: contig_output) 0:00:01.986 6M / 1359M INFO General (contig_output.hpp : 16) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/before_rr.fasta 0:00:01.990 6M / 1359M INFO General (contig_output_stage.cpp : 151) Writing GFA graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/assembly_graph_with_scaffolds.gfa 0:00:01.991 6M / 1359M INFO General (contig_output_stage.cpp : 165) Outputting FastG graph to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/assembly_graph.fastg 0:00:01.995 6M / 1359M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/transcripts.fasta 0:00:01.996 6M / 1359M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/transcripts.paths 0:00:01.997 6M / 1359M INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 0:00:01.998 6M / 1359M INFO General (pipeline.cpp : 287) SPAdes finished 0:00:01.999 1M / 1359M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 2 seconds ===== K73 finished. ===== Copy files started. == Running: /usr/bin/python /SPAdes-3.15.2-Linux/share/spades/spades_pipeline/scripts/copy_files.py /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/before_rr.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/before_rr.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/assembly_graph_after_simplification.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/assembly_graph_after_simplification.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/transcripts.paths /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/transcripts.paths /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/assembly_graph_with_scaffolds.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/assembly_graph_with_scaffolds.gfa /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/assembly_graph.fastg /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/assembly_graph.fastg /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/hard_filtered_final_paths.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/hard_filtered_transcripts.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/K73/soft_filtered_final_paths.fasta /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/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/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/scaffolds.fasta --misc_dir /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/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/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/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/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/transcripts.paths * Hard filtered transcripts are in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/hard_filtered_transcripts.fasta * Soft filtered transcripts are in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/soft_filtered_transcripts.fasta * Assembly graph is in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/assembly_graph.fastg * Assembly graph in GFA format is in /pscratch/sd/n/nmjaws/nmdc-prod/cromwell-executions/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/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/metaT/41a6c2fc-8b0b-4a18-84e3-a13f3d592147/call-asse/metatranscriptome_assy/8bcf2c17-0505-42ad-8bb0-150c4c889656/call-assy/execution/out.spades/spades.log Thank you for using SPAdes!