Command line: /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/bin/spades.py --isolate --cov-cutoff auto -t 10 -k 21,33,55,77,99,127 -m 28 -1 /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/0_trim/FAM24227-i1-2_1.fastq.gz -2 /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/0_trim/FAM24227-i1-2_2.fastq.gz -o /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly System information: SPAdes version: 3.14.0 Python version: 3.8.3 OS: Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-glibc2.10 Output dir: /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly Mode: ONLY assembling (without read error correction) Debug mode is turned OFF Dataset parameters: Isolate mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/0_trim/FAM24227-i1-2_1.fastq.gz'] right reads: ['/data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/0_trim/FAM24227-i1-2_2.fastq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Assembly parameters: k: [21, 33, 55, 77, 99, 127] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned ON and threshold will be auto-detected Other parameters: Dir for temp files: /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/tmp Threads: 10 Memory limit (in Gb): 28 ======= SPAdes pipeline started. Log can be found here: /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/spades.log /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/0_trim/FAM24227-i1-2_1.fastq.gz: max reads length: 151 /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/0_trim/FAM24227-i1-2_2.fastq.gz: max reads length: 151 Reads length: 151 ===== Assembling started. ===== K21 started. == Running: /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/bin/spades-core /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K21/configs/config.info /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K21/configs/isolate_mode.info 0:00:00.000 5M / 11M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K21/configs/config.info 0:00:00.000 5M / 11M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K21/configs/isolate_mode.info 0:00:00.000 5M / 12M INFO General (memory_limit.cpp : 49) Memory limit set to 28 Gb 0:00:00.000 5M / 12M INFO General (main.cpp : 83) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 5M / 12M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.000 5M / 12M INFO General (main.cpp : 85) Assembling dataset (/data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/dataset.info) with K=21 0:00:00.001 5M / 12M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 10 0:00:00.001 5M / 12M INFO General (launch.hpp : 79) SPAdes started 0:00:00.001 5M / 12M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.001 5M / 12M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.001 5M / 12M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.003 5M / 14M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.003 5M / 14M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:01.119 189M / 189M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:01.214 206M / 206M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:01.402 241M / 254M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:01.770 283M / 314M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:02.578 376M / 412M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:04.214 466M / 502M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:00:08.115 588M / 628M INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:00:16.310 537M / 665M INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:00:28.966 626M / 690M INFO General (binary_converter.cpp : 111) 3820875 reads written 0:00:28.967 602M / 690M INFO General (read_converter.cpp : 81) Converting single reads 0:00:28.969 612M / 690M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:28.969 602M / 690M INFO General (read_converter.cpp : 87) Converting merged reads 0:00:28.971 612M / 690M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:29.014 85M / 690M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:29.041 85M / 690M INFO General (construction.cpp : 150) Max read length 151 0:00:29.042 85M / 690M INFO General (construction.cpp : 156) Average read length 133.845 0:00:29.042 85M / 690M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:29.044 85M / 690M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:29.045 85M / 690M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:29.046 85M / 690M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933284 Gb 0:00:29.046 85M / 690M INFO General (kmer_splitters.hpp : 97) Using cell size of 671088 0:00:42.986 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 11677474 reads 0:00:48.980 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 15283500 reads 0:00:49.086 113M / 7G INFO General (kmer_splitters.hpp : 293) Used 15283500 reads 0:00:49.086 113M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:50.555 113M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 15989122 kmers in total. 0:00:50.555 113M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:51.309 93M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:51.310 93M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:51.310 93M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:51.311 93M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:51.311 93M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933271 Gb 0:00:51.311 93M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 419430 0:00:52.654 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 15989122 kmers 0:00:52.654 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 15989122 kmers. 0:00:52.791 94M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:53.299 94M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 15517031 kmers in total. 0:00:53.300 94M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:53.791 94M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:54.589 79M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:54.755 79M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 7203328 bytes occupied (3.71377 bits per kmer). 0:00:54.767 95M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:55.559 95M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:55.562 83M / 7G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping 0:00:55.563 83M / 7G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) 0:00:55.563 83M / 7G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping 0:00:56.832 103M / 7G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 284240 0:00:56.855 103M / 7G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 292165 0:00:56.863 103M / 7G INFO Early tip clipping (early_simplification.hpp : 30) 2980929 22-mers were removed by early tip clipper 0:00:56.863 103M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:56.891 103M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:57.980 188M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1294132 sequences extracted 0:00:58.605 188M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:58.903 188M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected 0:01:00.538 452M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:01:00.539 452M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:00.539 452M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:01.716 452M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 7419224 bytes occupied (3.71214 bits per kmer). 0:01:01.742 516M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:01:21.536 489M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:01:22.425 489M / 7G INFO General (construction.cpp : 505) Processed 2588185 edges 0:01:22.476 402M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:01:22.477 402M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 39 0:01:22.477 402M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 341 0:01:22.477 402M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 341. Coverage mad: 62.2692 0:01:22.477 402M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:22.784 402M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:23.601 395M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:26.468 395M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:30.214 394M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 327.983. Fitted coverage std. dev: 67.8433 0:01:30.227 394M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.18751 0:01:30.227 394M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 52 0:01:30.227 394M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 52 0:01:30.227 394M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2479667 0:01:30.228 394M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 327.983 0:01:30.228 394M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 52 0:01:30.228 394M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 7 0:01:30.228 394M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:01:30.228 394M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:01:30.229 394M / 7G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled 0:01:30.229 394M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:01:30.309 394M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:01:30.309 394M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:01:30.309 394M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:01:30.310 394M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:30.310 394M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:01:30.310 394M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:30.461 352M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1596 times 0:01:30.462 352M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:02.926 368M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 444666 times 0:02:02.926 368M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:03.591 346M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 31835 times 0:02:03.591 346M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:02:03.591 346M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:03.603 346M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 457 times 0:02:03.603 346M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.509 345M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 203 times 0:02:04.509 345M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.576 339M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3272 times 0:02:04.577 339M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:02:04.577 339M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.578 339M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times 0:02:04.578 339M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.603 339M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19 times 0:02:04.603 339M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.634 335M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1290 times 0:02:04.634 335M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:02:04.634 335M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.635 335M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:02:04.635 335M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.643 335M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 13 times 0:02:04.643 335M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.659 334M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 618 times 0:02:04.659 334M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:02:04.660 334M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.660 334M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:02:04.660 334M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.664 334M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times 0:02:04.664 334M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.674 333M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 342 times 0:02:04.674 333M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:02:04.675 333M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.675 333M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:02:04.675 333M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.677 333M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times 0:02:04.678 333M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.684 333M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 187 times 0:02:04.684 333M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:02:04.684 333M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.684 333M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:04.685 333M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.686 333M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:02:04.686 333M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.691 332M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 130 times 0:02:04.691 332M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:02:04.692 332M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.692 332M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:02:04.692 332M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.693 332M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:04.693 332M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.695 332M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 80 times 0:02:04.695 332M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:02:04.696 332M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.696 332M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:02:04.696 332M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.697 332M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:02:04.697 332M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.699 331M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 46 times 0:02:04.699 331M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:02:04.700 331M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.700 331M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:04.700 331M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.700 331M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:04.701 331M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.702 331M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 47 times 0:02:04.702 331M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:02:04.703 331M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.714 331M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 17 times 0:02:04.714 331M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.729 331M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:02:04.729 331M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.739 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:02:04.740 330M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:02:04.740 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.740 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:04.740 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.740 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:04.741 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:04.741 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:02:04.749 330M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:02:04.750 330M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:02:04.750 330M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:02:04.750 330M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:02:04.750 330M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:02:04.751 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.760 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:04.760 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.773 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:04.773 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:04.783 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:04.783 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:04.796 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:04.796 330M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:02:04.811 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:02:04.850 326M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 11499 times 0:02:04.851 326M / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 7 and less 0:02:04.859 326M / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:02:04.866 326M / 7G INFO General (simplification.cpp : 502) Average coverage = 346.265 0:02:04.866 326M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:02:04.867 326M / 7G INFO General (read_converter.cpp : 102) Outputting contigs to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K21/simplified_contigs 0:02:04.878 330M / 7G INFO General (binary_converter.cpp : 111) 2224 reads written 0:02:04.882 330M / 7G INFO General (launch.hpp : 192) SPAdes finished 0:02:04.897 268M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 2 minutes 4 seconds ===== K21 finished. ===== K33 started. == Running: /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/bin/spades-core /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K33/configs/config.info /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K33/configs/isolate_mode.info 0:00:00.000 5M / 11M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K33/configs/config.info 0:00:00.000 5M / 11M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K33/configs/isolate_mode.info 0:00:00.000 5M / 12M INFO General (memory_limit.cpp : 49) Memory limit set to 28 Gb 0:00:00.000 5M / 12M INFO General (main.cpp : 83) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 5M / 12M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.001 5M / 12M INFO General (main.cpp : 85) Assembling dataset (/data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/dataset.info) with K=33 0:00:00.001 5M / 12M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 10 0:00:00.001 5M / 12M INFO General (launch.hpp : 79) SPAdes started 0:00:00.001 5M / 12M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.001 5M / 12M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.001 5M / 12M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.003 5M / 14M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.005 6M / 16M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:00.005 6M / 16M INFO General (construction.cpp : 115) Contigs from previous K will be used: /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K21/simplified_contigs 0:00:00.051 6M / 16M INFO General (construction.cpp : 150) Max read length 151 0:00:00.051 6M / 16M INFO General (construction.cpp : 156) Average read length 133.845 0:00:00.051 6M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.052 6M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:00.052 6M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.052 6M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933302 Gb 0:00:00.052 6M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 335544 0:00:08.043 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 6569761 reads 0:00:16.355 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 13114632 reads 0:00:19.593 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 15287948 reads 0:00:19.722 108M / 7G INFO General (kmer_splitters.hpp : 293) Used 15287948 reads 0:00:19.722 108M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:22.024 108M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 20524437 kmers in total. 0:00:22.024 108M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:23.480 78M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:23.480 78M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:23.481 78M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:23.481 78M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:23.481 78M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933266 Gb 0:00:23.482 78M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:00:25.118 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 20524437 kmers 0:00:25.119 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 20524437 kmers. 0:00:25.264 84M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:25.904 76M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 20213626 kmers in total. 0:00:25.904 76M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:26.731 76M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:27.843 60M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:28.313 60M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9381176 bytes occupied (3.71281 bits per kmer). 0:00:28.331 80M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:29.416 80M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:29.418 77M / 7G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping 0:00:29.419 77M / 7G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) 0:00:29.419 77M / 7G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping 0:00:31.308 88M / 7G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 367603 0:00:31.344 88M / 7G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 380240 0:00:31.358 88M / 7G INFO Early tip clipping (early_simplification.hpp : 30) 5806522 34-mers were removed by early tip clipper 0:00:31.358 88M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:31.366 86M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:32.754 159M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 971771 sequences extracted 0:00:33.501 159M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:33.920 159M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:35.048 368M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:35.049 368M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:35.049 368M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:35.682 368M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9522080 bytes occupied (3.71151 bits per kmer). 0:00:35.720 448M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:00:55.116 440M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:00:56.094 440M / 7G INFO General (construction.cpp : 505) Processed 1943493 edges 0:00:56.179 340M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:00:56.180 340M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 27 0:00:56.180 340M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 302 0:00:56.180 340M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 302. Coverage mad: 57.8214 0:00:56.181 340M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:56.451 340M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:57.175 340M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:59.604 340M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:03.145 340M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 291.355. Fitted coverage std. dev: 61.177 0:01:03.156 340M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.240496 0:01:03.156 340M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 38 0:01:03.157 340M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 38 0:01:03.157 340M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2485946 0:01:03.157 340M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 291.355 0:01:03.157 340M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 38 0:01:03.158 340M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 6 0:01:03.158 340M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:01:03.158 340M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:01:03.158 340M / 7G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled 0:01:03.159 340M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:01:03.214 340M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:01:03.215 340M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:01:03.215 340M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:01:03.215 340M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:03.216 340M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:01:03.216 340M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:03.357 290M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5444 times 0:01:03.358 290M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:24.760 293M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 330253 times 0:01:24.761 293M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:24.998 291M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8901 times 0:01:24.998 291M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:01:24.999 291M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.027 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 630 times 0:01:25.027 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.039 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 212 times 0:01:25.039 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.051 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 219 times 0:01:25.051 292M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:01:25.051 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.052 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 10 times 0:01:25.052 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.053 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:01:25.053 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.057 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 43 times 0:01:25.057 292M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:01:25.057 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.057 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:01:25.058 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.058 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9 times 0:01:25.059 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.060 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 15 times 0:01:25.060 292M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:01:25.060 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.061 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:25.061 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.061 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:01:25.061 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.062 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times 0:01:25.063 292M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:01:25.063 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.063 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:25.063 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.064 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:01:25.064 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.064 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times 0:01:25.065 292M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:01:25.065 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.065 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:25.065 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.066 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:25.066 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.066 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times 0:01:25.066 292M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:01:25.066 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.067 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:25.067 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.067 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:01:25.067 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.068 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times 0:01:25.068 292M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:01:25.068 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.068 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:25.069 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.069 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:25.069 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.069 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:01:25.070 292M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:01:25.070 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.070 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:25.070 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.071 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:25.071 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.071 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times 0:01:25.071 292M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:01:25.072 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.085 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 0:01:25.086 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.098 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 0:01:25.098 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.108 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:25.108 292M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:01:25.109 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.109 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:25.109 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.109 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:25.109 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.110 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:25.121 292M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:01:25.121 292M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:01:25.121 292M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:01:25.121 292M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:01:25.122 292M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:25.122 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.133 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:25.133 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.144 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:25.144 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.155 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:25.155 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.165 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:25.166 292M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:01:25.193 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:01:25.278 290M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 29229 times 0:01:25.279 290M / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 6 and less 0:01:25.285 290M / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:01:25.290 290M / 7G INFO General (simplification.cpp : 502) Average coverage = 308.098 0:01:25.290 290M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:25.291 290M / 7G INFO General (read_converter.cpp : 102) Outputting contigs to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K33/simplified_contigs 0:01:25.299 294M / 7G INFO General (binary_converter.cpp : 111) 994 reads written 0:01:25.302 294M / 7G INFO General (launch.hpp : 192) SPAdes finished 0:01:25.313 246M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 1 minutes 25 seconds ===== K33 finished. ===== K55 started. == Running: /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/bin/spades-core /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K55/configs/config.info /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K55/configs/isolate_mode.info 0:00:00.000 5M / 11M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K55/configs/config.info 0:00:00.000 5M / 11M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K55/configs/isolate_mode.info 0:00:00.000 5M / 12M INFO General (memory_limit.cpp : 49) Memory limit set to 28 Gb 0:00:00.000 5M / 12M INFO General (main.cpp : 83) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 5M / 12M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.000 5M / 12M INFO General (main.cpp : 85) Assembling dataset (/data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/dataset.info) with K=55 0:00:00.000 5M / 12M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 10 0:00:00.000 5M / 12M INFO General (launch.hpp : 79) SPAdes started 0:00:00.001 5M / 12M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.001 5M / 12M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.001 5M / 12M INFO General (launch.hpp : 103) Will need read mapping, kmer mapper will be attached 0:00:00.001 5M / 12M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.004 5M / 14M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.005 6M / 16M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:00.005 6M / 16M INFO General (construction.cpp : 115) Contigs from previous K will be used: /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K33/simplified_contigs 0:00:00.079 6M / 16M INFO General (construction.cpp : 150) Max read length 151 0:00:00.079 6M / 16M INFO General (construction.cpp : 156) Average read length 133.845 0:00:00.079 6M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.080 6M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:00.081 6M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.081 6M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933302 Gb 0:00:00.081 6M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 335544 0:00:08.677 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 8264854 reads 0:00:16.147 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 15285488 reads 0:00:16.280 115M / 7G INFO General (kmer_splitters.hpp : 293) Used 15285488 reads 0:00:16.281 115M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:18.740 115M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 24652285 kmers in total. 0:00:18.741 115M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:20.135 85M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:20.136 85M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:20.136 85M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:20.137 85M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:20.137 85M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933271 Gb 0:00:20.137 85M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:00:22.170 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 24652285 kmers 0:00:22.170 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 24652285 kmers. 0:00:22.350 100M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:23.519 95M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 24566448 kmers in total. 0:00:23.519 95M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:27.418 95M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:28.514 71M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:29.122 71M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 11399496 bytes occupied (3.71222 bits per kmer). 0:00:29.140 95M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:30.467 95M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:30.468 95M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:30.486 95M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:34.296 238M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1374376 sequences extracted 0:00:35.517 238M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:36.015 238M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:38.049 557M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:38.050 557M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:38.050 557M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:38.832 557M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 11436312 bytes occupied (3.71124 bits per kmer). 0:00:38.874 653M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:00:54.647 611M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:00:56.258 611M / 7G INFO General (construction.cpp : 505) Processed 2748732 edges 0:00:56.400 491M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:00:56.401 491M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 26 0:00:56.401 491M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 237 0:00:56.401 491M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 237. Coverage mad: 47.4432 0:00:56.401 491M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:56.561 491M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:56.953 491M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:59.016 491M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:02.426 491M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 227.704. Fitted coverage std. dev: 49.7464 0:01:02.436 491M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.0125292 0:01:02.436 491M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 26 0:01:02.437 491M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 26 0:01:02.437 491M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2493333 0:01:02.437 491M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 227.704 0:01:02.437 491M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 26 0:01:02.438 491M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 4 0:01:02.438 491M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:01:02.438 491M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:01:02.440 491M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:02.440 491M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:01:02.441 491M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:02.442 491M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.920564 Gb 0:01:02.442 491M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:01:04.326 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 2748732 edges 0:01:04.327 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 2748732 sequences. 0:01:04.429 483M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:06.491 483M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 24652285 kmers in total. 0:01:06.491 483M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:07.743 483M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:09.023 484M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:09.595 484M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 11439288 bytes occupied (3.7122 bits per kmer). 0:01:09.732 868M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:01:10.776 865M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:01:10.834 865M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:01:12.625 944M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:31.271 900M / 7G INFO General (gap_closer.cpp : 126) Used 3820875 paired reads 0:01:31.272 900M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:31.491 881M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:32.979 882M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 6 gaps after checking 286 candidates 0:01:33.032 882M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:01:33.038 498M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:01:33.038 498M / 7G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled 0:01:33.039 498M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:01:33.137 498M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:01:33.137 498M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:01:33.137 498M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:01:33.138 498M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:33.138 498M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:01:33.138 498M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:37.055 466M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 505644 times 0:01:37.055 466M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:08.880 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 135318 times 0:02:08.881 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:08.979 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3455 times 0:02:08.980 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:02:08.980 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.014 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 928 times 0:02:09.015 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.053 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 158 times 0:02:09.053 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.062 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 149 times 0:02:09.062 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:02:09.063 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.063 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6 times 0:02:09.063 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.066 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9 times 0:02:09.066 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.069 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 51 times 0:02:09.069 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:02:09.069 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.069 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:02:09.070 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.071 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4 times 0:02:09.071 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.073 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 20 times 0:02:09.073 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:02:09.074 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.074 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:09.074 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.075 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:02:09.075 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.076 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times 0:02:09.076 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:02:09.076 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.077 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:02:09.077 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.077 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:02:09.078 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.078 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8 times 0:02:09.078 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:02:09.078 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.079 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:09.079 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.079 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:02:09.080 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.080 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times 0:02:09.081 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:02:09.081 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.081 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:09.081 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.082 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:09.082 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.082 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:02:09.082 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:02:09.083 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.083 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:09.083 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.083 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:09.083 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.084 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times 0:02:09.084 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:02:09.084 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.085 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:09.085 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.085 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:09.085 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.086 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:02:09.086 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:02:09.086 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.107 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times 0:02:09.107 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.122 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:09.122 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.137 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:02:09.137 2G / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:02:09.137 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:09.137 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:09.137 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:09.138 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:09.138 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:09.138 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:02:09.162 2G / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:02:09.162 2G / 7G INFO General (graph_pack.hpp : 105) Index refill 0:02:09.164 2G / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:02:09.164 2G / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:02:09.166 2G / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:02:09.166 2G / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.899008 Gb 0:02:09.167 2G / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:02:09.603 8G / 8G INFO General (edge_index_builders.hpp : 77) Processed 108248 edges 0:02:09.603 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 108248 sequences. 0:02:09.650 2G / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:02:09.843 2G / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3598037 kmers in total. 0:02:09.843 2G / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:02:10.122 2G / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:02:10.286 2G / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:02:10.375 2G / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1677000 bytes occupied (3.7287 bits per kmer). 0:02:10.400 2G / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:02:10.573 2G / 7G INFO General (edge_index.hpp : 92) Index refilled 0:02:10.618 2G / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:02:10.779 2G / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:02:22.391 2G / 7G INFO General (gap_closer.cpp : 126) Used 3820875 paired reads 0:02:22.392 2G / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:02:22.429 2G / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:02:22.536 2G / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 1 gaps after checking 42 candidates 0:02:22.581 2G / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:02:22.581 2G / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:02:22.582 2G / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:02:22.582 2G / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:02:22.583 2G / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:02:22.583 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:22.616 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:22.616 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:22.643 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:22.643 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:22.668 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:22.668 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:22.690 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:22.690 2G / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:02:22.784 2G / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:02:23.698 2G / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 53545 times 0:02:23.698 2G / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 4 and less 0:02:23.708 2G / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:02:23.714 2G / 7G INFO General (simplification.cpp : 502) Average coverage = 239.86 0:02:23.715 2G / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:02:23.716 2G / 7G INFO General (read_converter.cpp : 102) Outputting contigs to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K55/simplified_contigs 0:02:23.723 2G / 7G INFO General (binary_converter.cpp : 111) 578 reads written 0:02:23.725 2G / 7G INFO General (launch.hpp : 192) SPAdes finished 0:02:26.840 1016M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 2 minutes 26 seconds ===== K55 finished. ===== K77 started. == Running: /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/bin/spades-core /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K77/configs/config.info /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K77/configs/isolate_mode.info 0:00:00.000 5M / 11M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K77/configs/config.info 0:00:00.000 5M / 11M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K77/configs/isolate_mode.info 0:00:00.000 5M / 12M INFO General (memory_limit.cpp : 49) Memory limit set to 28 Gb 0:00:00.001 5M / 12M INFO General (main.cpp : 83) Starting SPAdes, built from N/A, git revision N/A 0:00:00.001 5M / 12M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.001 5M / 12M INFO General (main.cpp : 85) Assembling dataset (/data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/dataset.info) with K=77 0:00:00.001 5M / 12M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 10 0:00:00.001 5M / 12M INFO General (launch.hpp : 79) SPAdes started 0:00:00.001 5M / 12M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.001 5M / 12M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.001 5M / 12M INFO General (launch.hpp : 103) Will need read mapping, kmer mapper will be attached 0:00:00.001 5M / 12M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.003 5M / 14M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.005 6M / 16M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:00.005 6M / 16M INFO General (construction.cpp : 115) Contigs from previous K will be used: /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K55/simplified_contigs 0:00:00.033 6M / 16M INFO General (construction.cpp : 150) Max read length 151 0:00:00.033 6M / 16M INFO General (construction.cpp : 156) Average read length 133.845 0:00:00.033 6M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.034 6M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:00.035 6M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.035 6M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933302 Gb 0:00:00.035 6M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 223696 0:00:06.720 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 7343884 reads 0:00:12.925 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 14613263 reads 0:00:16.406 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 15284656 reads 0:00:16.546 171M / 7G INFO General (kmer_splitters.hpp : 293) Used 15284656 reads 0:00:16.546 171M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:20.089 159M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 24345612 kmers in total. 0:00:20.089 159M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:23.246 159M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:23.246 159M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:23.247 159M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:23.249 93M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:23.249 93M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933267 Gb 0:00:23.249 93M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 0:00:26.915 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 24345612 kmers 0:00:26.916 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 24345612 kmers. 0:00:27.121 151M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:31.441 145M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 24433844 kmers in total. 0:00:31.442 145M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:37.732 145M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:39.844 143M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:42.089 143M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 11338088 bytes occupied (3.71226 bits per kmer). 0:00:42.109 167M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:43.395 167M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:43.397 165M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:43.417 165M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:47.592 183M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1139284 sequences extracted 0:00:48.761 183M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:49.272 183M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:50.901 452M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:50.902 452M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:50.902 452M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:51.671 452M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 11294232 bytes occupied (3.7113 bits per kmer). 0:00:51.710 548M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:01:04.398 544M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:01:06.047 544M / 7G INFO General (construction.cpp : 505) Processed 2278556 edges 0:01:06.221 419M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:01:06.222 419M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 20 0:01:06.222 419M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 174 0:01:06.222 419M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 174. Coverage mad: 38.5476 0:01:06.222 419M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:06.415 419M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:06.962 419M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:08.827 419M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:10.717 419M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 168.971. Fitted coverage std. dev: 38.6011 0:01:10.725 419M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.00251067 0:01:10.725 419M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 20 0:01:10.726 419M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 20 0:01:10.726 419M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2498541 0:01:10.726 419M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 168.971 0:01:10.726 419M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 20 0:01:10.727 419M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 3 0:01:10.727 419M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:01:10.727 419M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:01:10.732 419M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:10.732 419M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:01:10.733 419M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:10.733 419M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.922279 Gb 0:01:10.733 419M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 0:01:13.012 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 2278556 edges 0:01:13.013 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 2278556 sequences. 0:01:13.087 452M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:16.332 444M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 24345612 kmers in total. 0:01:16.333 444M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:17.553 444M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:19.038 435M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:20.821 435M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 11297264 bytes occupied (3.7123 bits per kmer). 0:01:20.956 819M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:01:21.949 819M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:01:21.992 819M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:01:23.567 918M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:35.008 857M / 7G INFO General (gap_closer.cpp : 126) Used 3820875 paired reads 0:01:35.009 857M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:35.268 840M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:36.530 861M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 8 gaps after checking 442 candidates 0:01:36.741 860M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:01:36.753 476M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:01:36.754 476M / 7G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled 0:01:36.754 476M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:01:36.870 476M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:01:36.870 476M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:01:36.870 476M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:01:36.871 476M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:36.871 476M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:01:36.871 476M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:41.652 419M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 543357 times 0:01:41.653 419M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.174 442M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5039 times 0:01:43.174 442M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.230 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 485 times 0:01:43.230 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:01:43.231 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.239 440M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 190 times 0:01:43.240 440M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.262 440M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 59 times 0:01:43.262 440M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.272 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 110 times 0:01:43.273 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:01:43.273 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.274 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9 times 0:01:43.274 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.279 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11 times 0:01:43.280 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.283 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 36 times 0:01:43.284 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:01:43.284 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.284 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:01:43.284 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.285 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.285 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.286 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times 0:01:43.286 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:01:43.286 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.287 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:43.287 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.287 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.288 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.289 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times 0:01:43.289 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:01:43.289 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.289 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:43.290 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.290 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.290 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.291 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times 0:01:43.291 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:01:43.292 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.292 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:43.292 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.293 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.293 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.293 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 0:01:43.294 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:01:43.294 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.294 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:43.294 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.295 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.295 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.295 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:01:43.295 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:01:43.296 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.296 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:43.296 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.297 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.297 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.297 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:43.297 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:01:43.298 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.298 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:43.298 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.298 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.299 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.299 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:43.299 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:01:43.299 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.338 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times 0:01:43.339 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.369 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.370 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.398 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:43.399 439M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:01:43.399 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.400 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:43.400 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.400 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.400 439M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:43.401 439M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:43.440 439M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:01:43.441 439M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:01:43.443 439M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:43.444 439M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:01:43.447 435M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:43.447 435M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.920442 Gb 0:01:43.448 435M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 0:01:44.288 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 189271 edges 0:01:44.288 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 189271 sequences. 0:01:44.325 447M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:44.830 447M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6287120 kmers in total. 0:01:44.830 447M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:45.397 447M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:45.715 443M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:45.914 443M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2923624 bytes occupied (3.72014 bits per kmer). 0:01:45.954 539M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:01:46.214 539M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:01:46.245 539M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:01:46.579 560M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:54.792 546M / 7G INFO General (gap_closer.cpp : 126) Used 3820875 paired reads 0:01:54.793 546M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:54.860 546M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:55.018 545M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 0 gaps after checking 52 candidates 0:01:55.066 545M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:01:55.067 545M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:01:55.067 545M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:01:55.067 545M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:01:55.068 545M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:55.069 545M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:55.113 545M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:55.113 545M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:55.147 545M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:55.148 545M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:55.181 545M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:55.182 545M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:55.209 545M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:55.210 545M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:01:55.361 545M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:01:58.095 525M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 94152 times 0:01:58.095 525M / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 3 and less 0:01:58.102 525M / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:01:58.107 525M / 7G INFO General (simplification.cpp : 502) Average coverage = 175.457 0:01:58.107 525M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:58.108 525M / 7G INFO General (read_converter.cpp : 102) Outputting contigs to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K77/simplified_contigs 0:01:58.117 526M / 7G INFO General (binary_converter.cpp : 111) 484 reads written 0:01:58.121 516M / 7G INFO General (launch.hpp : 192) SPAdes finished 0:01:58.216 335M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 1 minutes 58 seconds ===== K77 finished. ===== K99 started. == Running: /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/bin/spades-core /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K99/configs/config.info /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K99/configs/isolate_mode.info 0:00:00.000 5M / 13M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K99/configs/config.info 0:00:00.000 5M / 13M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K99/configs/isolate_mode.info 0:00:00.000 5M / 14M INFO General (memory_limit.cpp : 49) Memory limit set to 28 Gb 0:00:00.000 5M / 14M INFO General (main.cpp : 83) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 5M / 14M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.001 5M / 14M INFO General (main.cpp : 85) Assembling dataset (/data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/dataset.info) with K=99 0:00:00.001 5M / 14M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 10 0:00:00.001 5M / 14M INFO General (launch.hpp : 79) SPAdes started 0:00:00.001 5M / 14M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.001 5M / 14M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.001 5M / 14M INFO General (launch.hpp : 103) Will need read mapping, kmer mapper will be attached 0:00:00.001 5M / 14M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.003 5M / 16M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.004 6M / 18M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:00.004 6M / 18M INFO General (construction.cpp : 115) Contigs from previous K will be used: /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K77/simplified_contigs 0:00:00.024 6M / 18M INFO General (construction.cpp : 150) Max read length 151 0:00:00.024 6M / 18M INFO General (construction.cpp : 156) Average read length 133.845 0:00:00.024 6M / 18M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.025 6M / 18M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:00.025 6M / 18M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.025 6M / 18M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933302 Gb 0:00:00.025 6M / 18M INFO General (kmer_splitters.hpp : 97) Using cell size of 167772 0:00:08.262 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 8085291 reads 0:00:15.706 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 15271628 reads 0:00:15.859 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 15284468 reads 0:00:15.955 118M / 7G INFO General (kmer_splitters.hpp : 293) Used 15284468 reads 0:00:15.955 118M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:19.955 118M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 20449143 kmers in total. 0:00:19.955 118M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:22.954 40M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:22.954 40M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:22.955 40M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:22.955 40M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:22.956 40M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933267 Gb 0:00:22.956 40M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:00:25.632 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 20449143 kmers 0:00:25.633 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 20449143 kmers. 0:00:25.849 29M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:30.368 29M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 20695565 kmers in total. 0:00:30.368 29M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:34.580 29M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:36.067 45M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:39.496 45M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9604792 bytes occupied (3.71279 bits per kmer). 0:00:39.509 65M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:40.973 65M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:40.975 64M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:40.990 64M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:44.540 174M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 944433 sequences extracted 0:00:45.758 174M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:46.233 174M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected 0:00:47.876 417M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:47.876 417M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:47.876 417M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:48.542 417M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9487200 bytes occupied (3.71153 bits per kmer). 0:00:48.577 497M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:00:57.765 495M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:00:59.204 495M / 7G INFO General (construction.cpp : 505) Processed 1888862 edges 0:00:59.368 395M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:00:59.369 395M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 12 0:00:59.369 395M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 116 0:00:59.369 395M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 116. Coverage mad: 28.1694 0:00:59.370 395M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:59.500 395M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:59.902 395M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:01.347 395M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:04.194 395M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:04.521 395M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 113.807. Fitted coverage std. dev: 27.5447 0:01:04.525 395M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.00490155 0:01:04.526 395M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 12 0:01:04.526 395M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 12 0:01:04.526 395M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2503095 0:01:04.526 395M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 113.807 0:01:04.526 395M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 12 0:01:04.527 395M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 3 0:01:04.527 395M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:01:04.527 395M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:01:04.529 395M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:04.529 395M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:01:04.530 395M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:04.530 395M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.923587 Gb 0:01:04.530 395M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:01:06.286 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 1888862 edges 0:01:06.287 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 1888862 sequences. 0:01:06.390 415M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:13.353 415M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 20449143 kmers in total. 0:01:13.354 415M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:31.267 415M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:34.959 413M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:37.589 413M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9490448 bytes occupied (3.7128 bits per kmer). 0:01:37.724 733M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:01:38.627 732M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:01:39.216 732M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:01:40.951 835M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:48.204 767M / 7G INFO General (gap_closer.cpp : 126) Used 3820875 paired reads 0:01:48.205 767M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:48.522 750M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:49.659 766M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 15 gaps after checking 475 candidates 0:01:50.081 764M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:01:50.092 444M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:01:50.092 444M / 7G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled 0:01:50.093 444M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:01:50.193 444M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:01:50.194 444M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:01:50.194 444M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:01:50.194 444M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:50.195 444M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:01:50.195 444M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.740 395M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 361597 times 0:01:53.740 395M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.837 396M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 138 times 0:01:53.837 396M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:53.893 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 101 times 0:01:53.893 370M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:01:53.893 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.896 371M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 65 times 0:01:53.896 371M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.901 371M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 12 times 0:01:53.901 371M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:53.904 371M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 54 times 0:01:53.904 371M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:01:53.905 371M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.905 371M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 0:01:53.905 371M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.908 371M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times 0:01:53.908 371M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:53.910 371M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 25 times 0:01:53.910 371M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:01:53.911 371M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.911 371M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:01:53.911 371M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.914 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times 0:01:53.914 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:53.915 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 15 times 0:01:53.915 370M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:01:53.915 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.916 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:01:53.916 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.917 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:01:53.917 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:53.917 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times 0:01:53.918 370M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:01:53.918 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.918 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:53.918 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.919 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:53.919 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:53.919 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times 0:01:53.919 370M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:01:53.920 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.920 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:01:53.920 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.921 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:53.921 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:53.921 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:01:53.921 370M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:01:53.922 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.922 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:53.922 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.922 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:53.922 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:53.923 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 0:01:53.923 370M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:01:53.923 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.923 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:53.924 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.924 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:53.924 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:53.925 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:01:53.925 370M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:01:53.925 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.925 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:53.925 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.926 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:53.926 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:53.926 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:53.926 370M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:01:53.927 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.995 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 33 times 0:01:53.995 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:54.045 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:01:54.046 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:54.093 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:54.094 370M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:01:54.094 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:54.094 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:54.095 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:54.095 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:54.095 370M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:54.095 370M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:54.136 370M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:01:54.136 370M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:01:54.138 370M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:54.138 370M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:01:54.230 370M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:54.231 370M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.922981 Gb 0:01:54.232 370M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:01:56.307 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 494717 edges 0:01:56.307 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 494717 sequences. 0:01:56.399 386M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:02:03.430 386M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12246963 kmers in total. 0:02:03.431 386M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:02:07.236 386M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:02:08.248 377M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:02:09.413 377M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5687016 bytes occupied (3.71489 bits per kmer). 0:02:09.502 569M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:02:10.020 569M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:02:10.091 569M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:02:10.927 625M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:02:15.310 601M / 7G INFO General (gap_closer.cpp : 126) Used 3820875 paired reads 0:02:15.311 601M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:02:15.487 593M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:02:15.871 593M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 0 gaps after checking 144 candidates 0:02:15.904 593M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:02:15.904 593M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:02:15.905 593M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:02:15.905 593M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:02:15.905 593M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:02:15.905 593M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:15.967 593M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:15.967 593M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:16.017 592M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:16.017 592M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:16.073 592M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:16.073 592M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:16.118 580M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:16.118 580M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:02:16.383 580M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:02:24.402 423M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 246926 times 0:02:24.402 423M / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 3 and less 0:02:24.411 423M / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:02:24.416 423M / 7G INFO General (simplification.cpp : 502) Average coverage = 118.036 0:02:24.416 423M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:02:24.437 423M / 7G INFO General (read_converter.cpp : 102) Outputting contigs to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K99/simplified_contigs 0:02:24.446 427M / 7G INFO General (binary_converter.cpp : 111) 429 reads written 0:02:24.451 425M / 7G INFO General (launch.hpp : 192) SPAdes finished 0:02:24.470 165M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 2 minutes 24 seconds ===== K99 finished. ===== K127 started. == Running: /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/bin/spades-core /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/configs/config.info /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/configs/isolate_mode.info 0:00:00.000 5M / 11M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/configs/config.info 0:00:00.000 5M / 11M INFO General (main.cpp : 73) Loaded config from /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/configs/isolate_mode.info 0:00:00.000 5M / 12M INFO General (memory_limit.cpp : 49) Memory limit set to 28 Gb 0:00:00.000 5M / 12M INFO General (main.cpp : 83) Starting SPAdes, built from N/A, git revision N/A 0:00:00.001 5M / 12M INFO General (main.cpp : 84) Maximum k-mer length: 128 0:00:00.001 5M / 12M INFO General (main.cpp : 85) Assembling dataset (/data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/dataset.info) with K=127 0:00:00.001 5M / 12M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 10 0:00:00.001 5M / 12M INFO General (launch.hpp : 79) SPAdes started 0:00:00.001 5M / 12M INFO General (launch.hpp : 86) Starting from stage: read_conversion 0:00:00.001 5M / 12M INFO General (launch.hpp : 92) Two-step RR enabled: 0 0:00:00.001 5M / 12M INFO General (launch.hpp : 103) Will need read mapping, kmer mapper will be attached 0:00:00.001 5M / 12M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion 0:00:00.003 5M / 14M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.004 6M / 16M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:00.004 6M / 16M INFO General (construction.cpp : 115) Contigs from previous K will be used: /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K99/simplified_contigs 0:00:00.047 6M / 16M INFO General (construction.cpp : 150) Max read length 151 0:00:00.047 6M / 16M INFO General (construction.cpp : 156) Average read length 133.845 0:00:00.047 6M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.047 6M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:00.048 6M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.048 6M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933302 Gb 0:00:00.048 6M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 167772 0:00:05.467 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 15284358 reads 0:00:05.596 128M / 7G INFO General (kmer_splitters.hpp : 293) Used 15284358 reads 0:00:05.597 128M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:06.068 128M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11463055 kmers in total. 0:00:06.069 128M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:06.803 116M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:06.803 116M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:06.804 116M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:06.804 116M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:06.805 116M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933271 Gb 0:00:06.805 116M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:00:08.385 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 11463055 kmers 0:00:08.385 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 11463055 kmers. 0:00:08.583 94M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:10.267 94M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11821834 kmers in total. 0:00:10.268 94M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:11.377 94M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:12.220 87M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:13.457 87M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5490024 bytes occupied (3.71518 bits per kmer). 0:00:13.468 99M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:14.095 99M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:14.096 83M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:14.104 83M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:16.661 140M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 688122 sequences extracted 0:00:17.378 140M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:17.659 140M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected 0:00:19.035 320M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:19.035 320M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:19.036 320M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:19.441 320M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5320560 bytes occupied (3.71319 bits per kmer). 0:00:19.456 368M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:00:23.574 364M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:00:24.318 361M / 7G INFO General (construction.cpp : 505) Processed 1376245 edges 0:00:24.546 301M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:00:24.547 301M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 4 0:00:24.547 301M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 47 0:00:24.547 301M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 48. Coverage mad: 14.826 0:00:24.548 301M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:24.613 301M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:24.779 301M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:25.393 301M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:26.817 301M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:00:27.100 301M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 48.2365. Fitted coverage std. dev: 13.4083 0:00:27.103 301M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.246034 0:00:27.103 301M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 6 0:00:27.103 301M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 6 0:00:27.103 301M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2507781 0:00:27.103 301M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 48.2365 0:00:27.104 301M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 6 0:00:27.104 301M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 1 0:00:27.104 301M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:00:27.104 301M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:00:27.106 301M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:27.106 301M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:27.107 301M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:27.107 301M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.925822 Gb 0:00:27.107 301M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:00:28.304 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 1376245 edges 0:00:28.305 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 1376245 sequences. 0:00:28.420 305M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:29.410 300M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11463055 kmers in total. 0:00:29.411 300M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:30.327 300M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:31.241 299M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:32.740 299M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5323528 bytes occupied (3.71526 bits per kmer). 0:00:32.811 491M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:33.378 491M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:00:33.425 491M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:00:34.825 601M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:00:38.100 576M / 7G INFO General (gap_closer.cpp : 126) Used 3820875 paired reads 0:00:38.101 576M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:00:38.415 556M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:00:39.228 571M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 17 gaps after checking 287 candidates 0:00:39.362 571M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:00:39.368 379M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:39.368 379M / 7G INFO General (simplification.cpp : 63) Most init cleaning disabled on main iteration 0:00:39.369 379M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:39.454 379M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:39.454 379M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:00:39.455 379M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:00:39.455 379M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:00:39.455 379M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:00:39.456 379M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.111 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 167732 times 0:00:41.111 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.187 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 55 times 0:00:41.188 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.241 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:41.242 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:00:41.242 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.242 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:41.243 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.243 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:41.243 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.245 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times 0:00:41.245 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:00:41.245 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.246 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times 0:00:41.246 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.247 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:00:41.247 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.247 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 0:00:41.248 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:00:41.248 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.248 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:41.248 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.254 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:00:41.254 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.255 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times 0:00:41.255 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:00:41.255 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.255 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:41.255 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.256 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:00:41.256 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.257 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 0:00:41.257 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:00:41.257 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.258 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:41.258 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.258 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:41.258 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.259 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:41.259 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:00:41.259 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.259 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:41.259 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.259 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:41.260 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.260 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:41.260 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:00:41.261 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.261 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:41.261 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.262 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:41.262 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.262 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:00:41.263 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:00:41.263 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.263 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:41.263 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.264 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:41.264 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.264 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:00:41.264 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:00:41.265 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.265 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:41.265 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.265 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:41.266 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.266 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:41.266 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:00:41.266 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.334 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times 0:00:41.335 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.387 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:00:41.388 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.442 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:41.442 355M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:00:41.443 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:41.443 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:41.443 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:41.443 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:41.444 355M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:41.444 355M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:41.488 355M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:00:41.489 355M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:00:41.490 355M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:41.491 355M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:41.493 355M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:41.494 355M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.925348 Gb 0:00:41.494 355M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:00:42.890 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 718665 edges 0:00:42.890 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 718665 sequences. 0:00:42.951 336M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:43.907 335M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 9766070 kmers in total. 0:00:43.908 335M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:44.669 335M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:45.457 316M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:45.924 316M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4536552 bytes occupied (3.71617 bits per kmer). 0:00:45.987 476M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:46.458 467M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:00:46.671 467M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:00:47.618 550M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:00:51.088 527M / 7G INFO General (gap_closer.cpp : 126) Used 3820875 paired reads 0:00:51.089 527M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:00:51.339 508M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:00:51.798 508M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 1 gaps after checking 237 candidates 0:00:51.863 508M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:00:51.864 508M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:51.864 508M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:00:51.865 508M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:00:51.865 508M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:00:51.866 508M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:51.952 508M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:51.952 508M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:52.003 508M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:52.004 508M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:52.070 508M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:52.071 508M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:52.122 508M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:52.122 508M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:00:52.407 507M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:59.239 358M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 358968 times 0:00:59.240 358M / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 1 and less 0:00:59.244 358M / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:00:59.248 358M / 7G INFO General (simplification.cpp : 502) Average coverage = 50.0975 0:00:59.248 358M / 7G INFO StageManager (stage.cpp : 166) STAGE == Mismatch Correction 0:00:59.248 358M / 7G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 17554 kmers to process 0:00:59.254 358M / 7G INFO General (graph_pack.hpp : 115) Normalizing done 0:01:05.557 298M / 7G INFO General (mismatch_shall_not_pass.hp: 195) Finished collecting potential mismatches positions 0:01:05.569 296M / 7G INFO General (mismatch_shall_not_pass.hp: 303) All edges processed 0:01:05.569 296M / 7G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides 0:01:05.570 296M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:05.571 296M / 7G INFO General (contig_output_stage.cpp : 107) Writing GFA to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/assembly_graph_with_scaffolds.gfa 0:01:05.661 296M / 7G INFO General (contig_output.hpp : 21) Outputting contigs to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/before_rr.fasta 0:01:05.752 296M / 7G INFO General (contig_output_stage.cpp : 118) Outputting FastG graph to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/assembly_graph.fastg 0:01:05.967 296M / 7G INFO General (contig_output.hpp : 21) Outputting contigs to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/final_contigs.fasta 0:01:06.016 296M / 7G INFO StageManager (stage.cpp : 166) STAGE == Paired Information Counting 0:01:06.026 296M / 7G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 17554 kmers to process 0:01:06.027 296M / 7G INFO General (graph_pack.hpp : 115) Normalizing done 0:01:06.031 296M / 7G INFO General (pair_info_count.cpp : 322) Min edge length for estimation: 42046 0:01:06.031 296M / 7G INFO General (pair_info_count.cpp : 333) Estimating insert size for library #0 0:01:06.032 296M / 7G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:01:06.152 472M / 7G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:01:07.296 437M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 200000 reads 0:01:07.321 437M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 400000 reads 0:01:07.348 437M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 600000 reads 0:01:07.375 436M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 800000 reads 0:01:07.421 436M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 1000000 reads 0:01:07.468 436M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 1200000 reads 0:01:09.457 433M / 7G INFO General (sequence_mapper_notifier.h: 94) Total 3820875 reads processed 0:01:09.760 433M / 7G INFO General (pair_info_count.cpp : 208) Edge pairs: 5670 0:01:09.760 433M / 7G INFO General (pair_info_count.cpp : 212) 1191821 paired reads (31.1924% of all) aligned to long edges 0:01:09.766 256M / 7G INFO General (pair_info_count.cpp : 356) Insert size = 453.543, deviation = 99.9668, left quantile = 334, right quantile = 584, read length = 151 0:01:09.766 256M / 7G INFO General (pair_info_count.cpp : 373) Filtering data for library #0 0:01:09.768 256M / 7G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:01:11.008 256M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 200000 reads 0:01:11.421 256M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 400000 reads 0:01:11.447 256M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 600000 reads 0:01:11.794 256M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 800000 reads 0:01:11.826 256M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 1000000 reads 0:01:11.872 256M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 1200000 reads 0:01:13.407 256M / 7G INFO General (sequence_mapper_notifier.h: 94) Total 3820875 reads processed 0:01:13.408 256M / 7G INFO General (pair_info_count.cpp : 385) Mapping library #0 0:01:13.409 256M / 7G INFO General (pair_info_count.cpp : 387) Mapping paired reads (takes a while) 0:01:13.409 256M / 7G INFO General (pair_info_count.cpp : 288) Left insert size quantile 334, right insert size quantile 584, filtering threshold 2, rounding threshold 0 0:01:13.427 265M / 7G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:01:14.682 267M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 200000 reads 0:01:14.691 267M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 400000 reads 0:01:14.714 267M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 600000 reads 0:01:14.721 267M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 800000 reads 0:01:14.750 267M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 1000000 reads 0:01:14.765 267M / 7G INFO General (sequence_mapper_notifier.h: 76) Processed 1200000 reads 0:01:16.431 267M / 7G INFO General (sequence_mapper_notifier.h: 94) Total 3820875 reads processed 0:01:16.439 267M / 7G INFO StageManager (stage.cpp : 166) STAGE == Distance Estimation 0:01:16.440 267M / 7G INFO General (distance_estimation.cpp : 174) Processing library #0 0:01:16.440 267M / 7G INFO General (distance_estimation.cpp : 150) Weight Filter Done 0:01:16.441 267M / 7G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:01:16.452 264M / 7G INFO General (distance_estimation.cpp : 35) Filtering info 0:01:16.452 264M / 7G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 3618 0:01:16.454 264M / 7G INFO General (pair_info_filters.hpp : 263) Done filtering 0:01:16.454 264M / 7G INFO General (distance_estimation.cpp : 157) Refining clustered pair information 0:01:16.456 264M / 7G INFO General (distance_estimation.cpp : 159) The refining of clustered pair information has been finished 0:01:16.457 264M / 7G INFO General (distance_estimation.cpp : 161) Improving paired information 0:01:16.472 264M / 7G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 276; contradictional = 92 0:01:16.486 264M / 7G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 9; contradictional = 12 0:01:16.486 264M / 7G INFO General (distance_estimation.cpp : 104) Filling scaffolding index 0:01:16.487 264M / 7G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:01:16.500 265M / 7G INFO General (distance_estimation.cpp : 35) Filtering info 0:01:16.500 265M / 7G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 1024 0:01:16.501 265M / 7G INFO General (pair_info_filters.hpp : 263) Done filtering 0:01:16.501 265M / 7G INFO General (distance_estimation.cpp : 183) Clearing raw paired index 0:01:16.502 265M / 7G INFO StageManager (stage.cpp : 166) STAGE == Repeat Resolving 0:01:16.502 265M / 7G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:01:16.503 265M / 7G INFO General (launcher.cpp : 538) ExSPAnder repeat resolving tool started 0:01:16.512 266M / 7G INFO General (launcher.cpp : 404) Creating main extenders, unique edge length = 2000 0:01:16.513 266M / 7G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 50.0975 0:01:16.516 266M / 7G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 50.0975 0:01:16.526 266M / 7G INFO General (extenders_logic.cpp : 519) Using 1 paired-end library 0:01:16.527 266M / 7G INFO General (extenders_logic.cpp : 520) Using 1 paired-end scaffolding library 0:01:16.527 266M / 7G INFO General (extenders_logic.cpp : 521) Using 0 single read libraries 0:01:16.527 266M / 7G INFO General (launcher.cpp : 432) Total number of extenders is 3 0:01:16.527 266M / 7G INFO General (path_extender.hpp : 894) Processed 0 paths from 354 (0%) 0:01:16.573 266M / 7G INFO General (path_extender.hpp : 894) Processed 36 paths from 354 (10%) 0:01:16.607 267M / 7G INFO General (path_extender.hpp : 894) Processed 72 paths from 354 (20%) 0:01:16.638 267M / 7G INFO General (path_extender.hpp : 894) Processed 108 paths from 354 (30%) 0:01:16.641 268M / 7G INFO General (path_extender.hpp : 892) Processed 128 paths from 354 (36%) 0:01:16.642 268M / 7G INFO General (path_extender.hpp : 894) Processed 144 paths from 354 (40%) 0:01:16.649 268M / 7G INFO General (path_extender.hpp : 894) Processed 180 paths from 354 (50%) 0:01:16.656 268M / 7G INFO General (path_extender.hpp : 894) Processed 216 paths from 354 (61%) 0:01:16.658 268M / 7G INFO General (path_extender.hpp : 894) Processed 252 paths from 354 (71%) 0:01:16.660 268M / 7G INFO General (path_extender.hpp : 892) Processed 256 paths from 354 (72%) 0:01:16.660 268M / 7G INFO General (path_extender.hpp : 894) Processed 288 paths from 354 (81%) 0:01:16.660 268M / 7G INFO General (path_extender.hpp : 894) Processed 324 paths from 354 (91%) 0:01:16.661 268M / 7G INFO General (launcher.cpp : 244) Finalizing paths 0:01:16.661 268M / 7G INFO General (launcher.cpp : 246) Deduplicating paths 0:01:16.664 268M / 7G INFO General (launcher.cpp : 250) Paths deduplicated 0:01:16.664 268M / 7G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:01:16.664 268M / 7G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:01:16.665 268M / 7G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:01:16.665 268M / 7G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:01:16.670 268M / 7G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:01:16.675 268M / 7G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:01:16.677 269M / 7G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:01:16.678 269M / 7G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:01:16.682 269M / 7G INFO General (launcher.cpp : 267) Paths finalized 0:01:16.683 269M / 7G INFO General (launcher.cpp : 439) Closing gaps in paths 0:01:16.684 269M / 7G INFO General (launcher.cpp : 467) Gap closing completed 0:01:16.688 269M / 7G INFO General (launcher.cpp : 296) Traversing tandem repeats 0:01:16.692 269M / 7G INFO General (launcher.cpp : 306) Traversed 1 loops 0:01:16.692 269M / 7G INFO General (launcher.cpp : 244) Finalizing paths 0:01:16.692 269M / 7G INFO General (launcher.cpp : 246) Deduplicating paths 0:01:16.693 269M / 7G INFO General (launcher.cpp : 250) Paths deduplicated 0:01:16.693 269M / 7G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:01:16.693 269M / 7G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:01:16.694 269M / 7G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:01:16.694 269M / 7G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:01:16.694 269M / 7G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:01:16.695 269M / 7G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:01:16.695 269M / 7G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:01:16.695 269M / 7G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:01:16.699 269M / 7G INFO General (launcher.cpp : 267) Paths finalized 0:01:16.699 269M / 7G INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished 0:01:16.702 269M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:16.702 269M / 7G INFO General (contig_output_stage.cpp : 107) Writing GFA to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/assembly_graph_with_scaffolds.gfa 0:01:16.741 269M / 7G INFO General (contig_output.hpp : 21) Outputting contigs to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/before_rr.fasta 0:01:16.787 269M / 7G INFO General (contig_output_stage.cpp : 118) Outputting FastG graph to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/assembly_graph.fastg 0:01:16.910 270M / 7G INFO General (contig_output_stage.cpp : 80) Outputting FastG paths to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/final_contigs.paths 0:01:16.969 271M / 7G INFO General (contig_output_stage.cpp : 80) Outputting FastG paths to /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/scaffolds.paths 0:01:17.030 272M / 7G INFO General (launch.hpp : 192) SPAdes finished 0:01:17.042 64M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 1 minutes 17 seconds ===== K127 finished. ===== Copy files started. == Running: /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/bin/python /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/share/spades/spades_pipeline/scripts/copy_files.py /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/before_rr.fasta /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/before_rr.fasta /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/final_contigs.fasta /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/contigs.fasta /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/first_pe_contigs.fasta /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/first_pe_contigs.fasta /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/scaffolds.fasta /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/scaffolds.fasta /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/scaffolds.paths /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/scaffolds.paths /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/assembly_graph_with_scaffolds.gfa /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/assembly_graph_with_scaffolds.gfa /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/assembly_graph.fastg /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/assembly_graph.fastg /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/K127/final_contigs.paths /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/contigs.paths ===== Copy files finished. ===== Assembling finished. ===== Breaking scaffolds started. == Running: /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/bin/python /mnt/apps/centos7/Conda/miniconda3/envs/spades_3.14.0/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/scaffolds.fasta --misc_dir /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/misc --threshold_for_breaking_scaffolds 3 ===== Breaking scaffolds finished. ===== Terminate started. ===== Terminate finished. * Assembled contigs are in /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/contigs.fasta * Assembled scaffolds are in /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/scaffolds.fasta * Paths in the assembly graph corresponding to the contigs are in /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/scaffolds.paths * Assembly graph is in /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/assembly_graph.fastg * Assembly graph in GFA format is in /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished. SPAdes log can be found here: /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24227-i1-2/1_spades_assembly/spades.log Thank you for using SPAdes!