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/FAM24235-i1-2/0_trim/FAM24235-i1-2_1.fastq.gz -2 /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24235-i1-2/0_trim/FAM24235-i1-2_2.fastq.gz -o /data/projects/p446_Dialact_Phoenix/2_analyses/A_illumina/202204_reassemblies_emmanuelle/test/genome-assembly-pipeline/src/results/FAM24235-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/FAM24235-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/FAM24235-i1-2/0_trim/FAM24235-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/FAM24235-i1-2/0_trim/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-i1-2/0_trim/FAM24235-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/FAM24235-i1-2/0_trim/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-i1-2/1_spades_assembly/dataset.info) with K=21 0:00:00.000 5M / 12M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 10 0:00:00.001 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 0:00:01.131 185M / 185M INFO General (binary_converter.cpp : 96) 16384 reads processed 0:00:01.225 206M / 206M INFO General (binary_converter.cpp : 96) 32768 reads processed 0:00:01.410 240M / 256M INFO General (binary_converter.cpp : 96) 65536 reads processed 0:00:01.765 274M / 300M INFO General (binary_converter.cpp : 96) 131072 reads processed 0:00:02.991 329M / 355M INFO General (binary_converter.cpp : 96) 262144 reads processed 0:00:04.542 436M / 475M INFO General (binary_converter.cpp : 96) 524288 reads processed 0:00:08.060 605M / 641M INFO General (binary_converter.cpp : 96) 1048576 reads processed 0:00:15.910 589M / 663M INFO General (binary_converter.cpp : 96) 2097152 reads processed 0:00:21.774 684M / 746M INFO General (binary_converter.cpp : 111) 2787806 reads written 0:00:21.775 660M / 746M INFO General (read_converter.cpp : 81) Converting single reads 0:00:21.776 670M / 746M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:21.777 670M / 746M INFO General (read_converter.cpp : 87) Converting merged reads 0:00:21.778 670M / 746M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:21.806 96M / 746M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:21.830 96M / 746M INFO General (construction.cpp : 150) Max read length 151 0:00:21.830 96M / 746M INFO General (construction.cpp : 156) Average read length 132.811 0:00:21.830 96M / 746M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:21.832 96M / 746M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:21.834 96M / 746M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:21.835 96M / 746M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933285 Gb 0:00:21.835 96M / 746M INFO General (kmer_splitters.hpp : 97) Using cell size of 671088 0:00:35.157 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 11151224 reads 0:00:35.299 122M / 7G INFO General (kmer_splitters.hpp : 293) Used 11151224 reads 0:00:35.299 122M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:35.767 87M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12378947 kmers in total. 0:00:35.768 87M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:36.076 87M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:36.076 87M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:36.076 87M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:36.077 87M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:36.077 87M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933272 Gb 0:00:36.078 87M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 419430 0:00:37.076 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 12378947 kmers 0:00:37.076 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 12378947 kmers. 0:00:37.234 91M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:37.522 91M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12036507 kmers in total. 0:00:37.523 91M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:37.848 91M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:38.373 94M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:38.511 94M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5589576 bytes occupied (3.71508 bits per kmer). 0:00:38.521 106M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:39.194 106M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:39.197 101M / 7G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping 0:00:39.197 101M / 7G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) 0:00:39.198 101M / 7G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping 0:00:40.088 122M / 7G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 210899 0:00:40.107 122M / 7G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 215604 0:00:40.114 122M / 7G INFO Early tip clipping (early_simplification.hpp : 30) 2138813 22-mers were removed by early tip clipper 0:00:40.114 122M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:40.122 122M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:40.894 168M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 966506 sequences extracted 0:00:41.373 168M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:41.599 168M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 2 loops collected 0:00:42.882 350M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:42.882 350M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:42.882 350M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:43.277 349M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5745296 bytes occupied (3.71295 bits per kmer). 0:00:43.293 397M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:00:57.859 397M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:00:58.432 392M / 7G INFO General (construction.cpp : 505) Processed 1932958 edges 0:00:58.495 326M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:00:58.496 326M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 25 0:00:58.497 326M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 197 0:00:58.497 326M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 203. Coverage mad: 44.478 0:00:58.497 326M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:58.763 326M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:59.454 326M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:01.902 326M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:04.400 326M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 204.653. Fitted coverage std. dev: 40.5921 0:01:04.408 326M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.971283 0:01:04.408 326M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 64 0:01:04.408 326M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 64 0:01:04.409 326M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2786765 0:01:04.409 326M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 204.653 0:01:04.409 326M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 64 0:01:04.409 326M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 13 0:01:04.410 326M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:01:04.410 326M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:01:04.410 326M / 7G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled 0:01:04.410 326M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:01:04.468 326M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:01:04.469 326M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:01:04.469 326M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:01:04.469 326M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:04.469 326M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:01:04.470 326M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:04.583 274M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1441 times 0:01:04.583 274M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:25.347 292M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 309997 times 0:01:25.348 292M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:25.949 277M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 35694 times 0:01:25.949 277M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:01:25.950 277M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:25.957 277M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 324 times 0:01:25.957 277M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.580 277M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 81 times 0:01:26.581 277M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.649 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3459 times 0:01:26.649 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:01:26.649 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.650 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 13 times 0:01:26.650 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.680 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times 0:01:26.681 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.705 271M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1087 times 0:01:26.705 271M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:01:26.706 271M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.706 271M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 10 times 0:01:26.706 271M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.714 271M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times 0:01:26.715 271M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.725 271M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 410 times 0:01:26.725 271M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:01:26.725 271M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.726 271M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:01:26.726 271M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.728 271M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4 times 0:01:26.728 271M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.733 271M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 200 times 0:01:26.734 271M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:01:26.734 271M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.734 271M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:26.734 271M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.736 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:01:26.736 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.739 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 120 times 0:01:26.740 270M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:01:26.740 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.740 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:01:26.740 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.741 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:01:26.741 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.743 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 82 times 0:01:26.743 270M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:01:26.743 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.744 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:01:26.744 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.744 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:01:26.744 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.746 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 65 times 0:01:26.746 270M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:01:26.746 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.747 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:26.747 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.747 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:01:26.748 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.748 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 22 times 0:01:26.749 270M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:01:26.749 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.749 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:26.749 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.750 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:01:26.750 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.751 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 38 times 0:01:26.751 270M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:01:26.751 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.761 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 18 times 0:01:26.762 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.772 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4 times 0:01:26.773 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.779 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:01:26.780 270M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:01:26.780 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.780 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:26.780 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.780 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:26.781 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:26.781 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:26.793 270M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:01:26.793 270M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:01:26.793 270M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:01:26.793 270M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:01:26.794 270M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:26.794 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.801 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:26.801 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.811 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:26.812 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:26.818 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:26.818 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:26.829 270M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:26.829 270M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:01:26.839 270M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:01:26.868 267M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 9668 times 0:01:26.868 267M / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 13 and less 0:01:26.873 267M / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:01:26.878 267M / 7G INFO General (simplification.cpp : 502) Average coverage = 222.722 0:01:26.878 267M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:26.966 267M / 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/FAM24235-i1-2/1_spades_assembly/K21/simplified_contigs 0:01:26.987 271M / 7G INFO General (binary_converter.cpp : 111) 2256 reads written 0:01:26.991 270M / 7G INFO General (launch.hpp : 192) SPAdes finished 0:01:27.017 219M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 1 minutes 27 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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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 0:00:00.000 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/FAM24235-i1-2/1_spades_assembly/dataset.info) with K=33 0:00:00.000 5M / 12M INFO General (main.cpp : 86) Maximum # of threads to use (adjusted due to OMP capabilities): 10 0:00:00.001 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 0:00:00.007 5M / 14M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.009 6M / 16M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:00.009 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/FAM24235-i1-2/1_spades_assembly/K21/simplified_contigs 0:00:00.187 6M / 16M INFO General (construction.cpp : 150) Max read length 151 0:00:00.187 6M / 16M INFO General (construction.cpp : 156) Average read length 132.811 0:00:00.188 6M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.190 6M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:00.196 6M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.196 6M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933302 Gb 0:00:00.196 6M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 335544 0:00:08.081 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 6594538 reads 0:00:20.317 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 11155736 reads 0:00:20.455 116M / 7G INFO General (kmer_splitters.hpp : 293) Used 11155736 reads 0:00:20.455 116M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:23.784 116M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 15576102 kmers in total. 0:00:23.785 116M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:25.977 56M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:25.978 56M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:25.978 56M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:25.979 56M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:25.979 56M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933271 Gb 0:00:25.979 56M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:00:28.018 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 15576102 kmers 0:00:28.018 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 15576102 kmers. 0:00:28.215 61M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:29.746 57M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 15361595 kmers in total. 0:00:29.746 57M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:31.317 57M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:32.229 57M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:33.022 57M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 7131472 bytes occupied (3.71392 bits per kmer). 0:00:33.039 73M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:33.785 73M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:33.788 73M / 7G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping 0:00:33.788 73M / 7G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) 0:00:33.789 73M / 7G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping 0:00:35.090 82M / 7G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 274254 0:00:35.110 82M / 7G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 281635 0:00:35.123 82M / 7G INFO Early tip clipping (early_simplification.hpp : 30) 4225925 34-mers were removed by early tip clipper 0:00:35.124 82M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:35.137 82M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:36.012 136M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 696857 sequences extracted 0:00:36.517 136M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:36.825 136M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:37.659 287M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:37.659 287M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:37.659 287M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:38.141 287M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 7227648 bytes occupied (3.71217 bits per kmer). 0:00:38.169 351M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:00:51.779 347M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:00:52.546 347M / 7G INFO General (construction.cpp : 505) Processed 1393680 edges 0:00:52.742 267M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:00:52.743 267M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 31 0:00:52.744 267M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 174 0:00:52.744 267M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 181. Coverage mad: 40.0302 0:00:52.744 267M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:53.000 267M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:53.710 267M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:56.263 267M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:58.754 267M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 181.797. Fitted coverage std. dev: 36.7586 0:00:58.762 267M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.519592 0:00:58.762 267M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 47 0:00:58.762 267M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 47 0:00:58.762 267M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2792622 0:00:58.763 267M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 181.797 0:00:58.763 267M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 47 0:00:58.763 267M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 10 0:00:58.763 267M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:00:58.763 267M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:58.764 267M / 7G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled 0:00:58.764 267M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:58.808 267M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 1 times 0:00:58.808 267M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:00:58.809 267M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:00:58.809 267M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:00:58.809 267M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:00:58.809 267M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:58.935 216M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5531 times 0:00:58.936 216M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.587 220M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 230280 times 0:01:11.587 220M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.727 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5683 times 0:01:11.728 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:01:11.728 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.750 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 430 times 0:01:11.750 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.755 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 78 times 0:01:11.755 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.760 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 110 times 0:01:11.760 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:01:11.760 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.761 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times 0:01:11.761 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.761 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:01:11.761 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.763 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 20 times 0:01:11.763 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:01:11.763 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.764 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:01:11.764 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.764 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.764 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.765 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times 0:01:11.765 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:01:11.765 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.765 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:01:11.766 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.766 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.766 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.767 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times 0:01:11.767 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:01:11.767 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.767 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:11.767 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.768 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.768 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.768 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:11.768 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:01:11.768 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.769 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:11.769 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.769 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.769 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.769 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:11.770 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:01:11.770 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.770 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:11.770 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.770 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.771 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.771 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:11.771 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:01:11.771 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.771 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:11.771 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.772 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.772 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.772 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:11.772 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:01:11.772 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.773 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:11.773 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.773 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.773 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.773 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:11.774 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:01:11.774 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.783 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6 times 0:01:11.783 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.791 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:01:11.792 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.798 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:11.799 219M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:01:11.799 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.799 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:11.799 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.799 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.800 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:11.800 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:11.811 219M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:01:11.811 219M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:01:11.811 219M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:01:11.811 219M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:01:11.812 219M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:11.812 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.819 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:11.819 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.827 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.827 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.834 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:11.834 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.842 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.842 219M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:01:11.856 219M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:01:11.898 219M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 22041 times 0:01:11.898 219M / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 10 and less 0:01:11.903 219M / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:01:11.906 219M / 7G INFO General (simplification.cpp : 502) Average coverage = 198.178 0:01:11.907 219M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:11.908 219M / 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/FAM24235-i1-2/1_spades_assembly/K33/simplified_contigs 0:01:11.915 223M / 7G INFO General (binary_converter.cpp : 111) 1051 reads written 0:01:11.918 222M / 7G INFO General (launch.hpp : 192) SPAdes finished 0:01:11.923 186M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 1 minutes 11 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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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 0:00:00.000 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/FAM24235-i1-2/1_spades_assembly/K33/simplified_contigs 0:00:00.054 6M / 16M INFO General (construction.cpp : 150) Max read length 151 0:00:00.054 6M / 16M INFO General (construction.cpp : 156) Average read length 132.811 0:00:00.054 6M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.055 6M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:00.055 6M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.055 6M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933302 Gb 0:00:00.055 6M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 335544 0:00:08.209 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 8322570 reads 0:00:11.666 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 11153326 reads 0:00:11.798 115M / 7G INFO General (kmer_splitters.hpp : 293) Used 11153326 reads 0:00:11.798 115M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:12.430 115M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 18398462 kmers in total. 0:00:12.431 115M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:14.321 97M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:14.322 97M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:14.322 97M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:14.322 97M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:14.323 97M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.93327 Gb 0:00:14.323 97M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:00:15.817 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 18398462 kmers 0:00:15.817 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 18398462 kmers. 0:00:15.951 87M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:16.503 87M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 18341128 kmers in total. 0:00:16.503 87M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:17.048 87M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:17.834 90M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:18.213 90M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8513088 bytes occupied (3.71322 bits per kmer). 0:00:18.225 110M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:19.091 110M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:19.092 98M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:19.109 98M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:20.635 163M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1004446 sequences extracted 0:00:21.445 163M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:21.811 163M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:23.340 402M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:23.340 402M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:23.340 402M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:23.899 402M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8536336 bytes occupied (3.71176 bits per kmer). 0:00:23.928 482M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:00:35.756 471M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:00:36.942 471M / 7G INFO General (construction.cpp : 505) Processed 2008887 edges 0:00:37.134 367M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:00:37.135 367M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 20 0:00:37.135 367M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 136 0:00:37.135 367M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 141. Coverage mad: 32.6172 0:00:37.136 367M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:37.340 367M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:37.896 367M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:39.932 367M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:42.365 367M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 142.214. Fitted coverage std. dev: 30.1304 0:00:42.371 367M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.330955 0:00:42.371 367M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 28 0:00:42.371 367M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 28 0:00:42.372 367M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2799398 0:00:42.372 367M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 142.214 0:00:42.372 367M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 28 0:00:42.372 367M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 6 0:00:42.373 367M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:00:42.373 367M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:00:42.375 367M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:42.375 367M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:42.376 367M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:42.377 367M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.924078 Gb 0:00:42.377 367M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:00:45.047 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 2008887 edges 0:00:45.048 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 2008887 sequences. 0:00:45.185 381M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:48.311 375M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 18398462 kmers in total. 0:00:48.311 375M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:50.728 375M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:51.690 360M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:52.551 360M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8539632 bytes occupied (3.71319 bits per kmer). 0:00:52.663 680M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:53.486 680M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:00:53.575 680M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:00:54.748 733M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:06.376 693M / 7G INFO General (gap_closer.cpp : 126) Used 2787806 paired reads 0:01:06.377 693M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:06.536 686M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:07.759 687M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 2 gaps after checking 186 candidates 0:01:07.854 703M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:01:07.862 383M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:01:07.863 383M / 7G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled 0:01:07.863 383M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:01:07.956 383M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:01:07.957 383M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:01:07.957 383M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:01:07.957 383M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:07.957 383M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:01:07.958 383M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.332 363M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 368089 times 0:01:11.332 363M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.489 792M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 93188 times 0:01:33.489 792M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.568 792M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2186 times 0:01:33.568 792M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:01:33.568 792M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.596 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 525 times 0:01:33.596 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.609 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 40 times 0:01:33.609 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.616 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 126 times 0:01:33.617 793M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:01:33.617 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.617 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:01:33.617 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.618 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:01:33.618 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.619 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 23 times 0:01:33.620 793M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:01:33.620 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.620 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:01:33.621 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.621 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:33.621 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.622 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13 times 0:01:33.622 793M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:01:33.623 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.623 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:33.623 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.623 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:33.624 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.625 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times 0:01:33.625 793M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:01:33.625 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.625 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:33.626 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.626 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:33.626 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.627 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:01:33.627 793M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:01:33.627 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.627 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:33.627 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.628 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:33.628 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.628 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:33.628 793M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:01:33.629 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.629 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:33.629 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.629 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:33.629 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.630 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 0:01:33.630 793M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:01:33.630 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.630 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:01:33.630 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.631 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:01:33.631 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.631 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:33.632 793M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:01:33.632 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.632 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:33.632 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.632 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:33.633 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.633 793M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:33.633 793M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:01:33.633 793M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.649 794M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5 times 0:01:33.650 794M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.660 794M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:33.661 794M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.671 794M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:33.671 794M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:01:33.671 794M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:33.672 794M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:33.672 794M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:33.672 794M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:33.672 794M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:33.673 794M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:33.689 794M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:01:33.689 794M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:01:33.691 794M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:33.691 794M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:01:33.692 794M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:33.692 794M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.908761 Gb 0:01:33.693 794M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:01:34.094 8G / 8G INFO General (edge_index_builders.hpp : 77) Processed 78207 edges 0:01:34.095 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 78207 sequences. 0:01:34.135 803M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:34.377 803M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3572794 kmers in total. 0:01:34.378 803M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:34.659 803M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:34.830 803M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:34.918 803M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1665032 bytes occupied (3.72825 bits per kmer). 0:01:34.945 859M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:01:35.094 855M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:01:35.163 855M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:01:35.293 865M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:43.201 863M / 7G INFO General (gap_closer.cpp : 126) Used 2787806 paired reads 0:01:43.201 863M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:43.230 862M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:43.312 859M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 0 gaps after checking 28 candidates 0:01:43.339 859M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:01:43.340 859M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:01:43.340 859M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:01:43.340 859M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:01:43.341 859M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:43.341 859M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.358 859M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:43.359 859M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.375 859M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.376 859M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:43.393 859M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:43.393 859M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:43.410 859M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:43.410 859M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:01:43.482 859M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:01:44.144 858M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 38468 times 0:01:44.145 858M / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 6 and less 0:01:44.152 858M / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:01:44.157 858M / 7G INFO General (simplification.cpp : 502) Average coverage = 154.407 0:01:44.157 858M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:44.158 858M / 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/FAM24235-i1-2/1_spades_assembly/K55/simplified_contigs 0:01:44.167 862M / 7G INFO General (binary_converter.cpp : 111) 633 reads written 0:01:44.169 862M / 7G INFO General (launch.hpp : 192) SPAdes finished 0:01:45.786 739M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 1 minutes 45 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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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 0:00:00.000 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/FAM24235-i1-2/1_spades_assembly/dataset.info) with K=77 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 0:00:00.003 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/FAM24235-i1-2/1_spades_assembly/K55/simplified_contigs 0:00:00.013 6M / 16M INFO General (construction.cpp : 150) Max read length 151 0:00:00.013 6M / 16M INFO General (construction.cpp : 156) Average read length 132.811 0:00:00.013 6M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.014 6M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:00.016 6M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.016 6M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933302 Gb 0:00:00.016 6M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 223696 0:00:06.316 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 7398427 reads 0:00:10.234 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 11152490 reads 0:00:10.367 117M / 7G INFO General (kmer_splitters.hpp : 293) Used 11152490 reads 0:00:10.367 117M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:14.073 117M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 18133081 kmers in total. 0:00:14.073 117M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:15.677 62M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:15.678 62M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:15.678 62M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:15.679 62M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:15.679 62M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933271 Gb 0:00:15.679 62M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 0:00:17.467 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 18133081 kmers 0:00:17.468 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 18133081 kmers. 0:00:17.650 101M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:19.382 89M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 18196202 kmers in total. 0:00:19.383 89M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:20.485 89M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:21.346 78M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:22.017 78M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8445848 bytes occupied (3.71324 bits per kmer). 0:00:22.035 98M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:22.953 98M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:22.954 98M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:22.970 98M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:24.684 155M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 825830 sequences extracted 0:00:25.523 155M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:25.906 155M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:27.170 355M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:27.171 355M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:27.171 355M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:27.749 355M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8413320 bytes occupied (3.71181 bits per kmer). 0:00:27.772 435M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:00:36.404 431M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:00:37.558 427M / 7G INFO General (construction.cpp : 505) Processed 1651657 edges 0:00:37.688 327M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:00:37.688 327M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 15 0:00:37.688 327M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 100 0:00:37.689 327M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 105. Coverage mad: 26.6868 0:00:37.689 327M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:37.785 327M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:38.007 327M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:38.914 327M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:40.064 327M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 105.504. Fitted coverage std. dev: 23.6646 0:00:40.068 327M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.0671824 0:00:40.068 327M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 17 0:00:40.068 327M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 17 0:00:40.069 327M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2804024 0:00:40.069 327M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 105.504 0:00:40.069 327M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 17 0:00:40.069 327M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 4 0:00:40.070 327M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:00:40.070 327M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:00:40.072 327M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:40.073 327M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:40.074 327M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:40.075 327M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.925286 Gb 0:00:40.075 327M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 0:00:41.827 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 1651657 edges 0:00:41.828 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 1651657 sequences. 0:00:41.938 326M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:54.182 326M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 18133081 kmers in total. 0:00:54.183 326M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:03.524 326M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:06.315 316M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:07.084 316M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8416560 bytes occupied (3.71324 bits per kmer). 0:01:07.184 636M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:01:07.943 636M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:01:08.134 636M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:01:09.412 717M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:16.246 674M / 7G INFO General (gap_closer.cpp : 126) Used 2787806 paired reads 0:01:16.247 674M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:16.447 656M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:17.466 670M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 11 gaps after checking 261 candidates 0:01:17.503 670M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:01:17.510 350M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:01:17.511 350M / 7G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled 0:01:17.511 350M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:01:17.577 350M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:01:17.578 350M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:01:17.578 350M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:01:17.578 350M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:17.578 350M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:01:17.579 350M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:21.504 315M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 391212 times 0:01:21.504 315M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.217 319M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2548 times 0:01:22.217 319M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.255 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 237 times 0:01:22.256 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:01:22.256 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.260 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 98 times 0:01:22.261 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.266 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10 times 0:01:22.266 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.276 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 114 times 0:01:22.276 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:01:22.277 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.277 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5 times 0:01:22.277 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.279 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times 0:01:22.279 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.281 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 25 times 0:01:22.281 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:01:22.281 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.281 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:22.282 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.283 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:01:22.283 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.284 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times 0:01:22.284 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:01:22.284 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.285 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:22.285 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.285 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:22.285 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.286 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 0:01:22.287 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:01:22.287 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.287 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:22.287 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.287 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:22.288 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.289 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times 0:01:22.289 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:01:22.289 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.290 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:22.290 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.290 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:22.290 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.291 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times 0:01:22.291 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:01:22.292 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.292 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:22.292 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.292 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:22.292 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.293 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 0:01:22.293 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:01:22.294 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.294 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:22.294 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.294 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:22.294 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.295 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:22.295 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:01:22.295 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.295 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:22.296 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.296 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:22.296 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.296 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:22.296 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:01:22.297 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.322 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 13 times 0:01:22.323 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.343 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:22.343 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.363 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:22.363 318M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:01:22.363 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:22.363 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:22.364 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:22.364 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:22.364 318M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:22.364 318M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:22.393 318M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:01:22.394 318M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:01:22.396 318M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:22.396 318M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:01:22.397 318M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:22.398 318M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.924414 Gb 0:01:22.399 318M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 0:01:23.329 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 133446 edges 0:01:23.330 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 133446 sequences. 0:01:23.363 332M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:23.872 332M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5416067 kmers in total. 0:01:23.873 332M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:25.242 332M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:26.031 320M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:26.303 320M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2519792 bytes occupied (3.72195 bits per kmer). 0:01:26.342 416M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:01:26.575 416M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:01:26.635 416M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:01:26.874 432M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:32.263 416M / 7G INFO General (gap_closer.cpp : 126) Used 2787806 paired reads 0:01:32.264 416M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:32.306 415M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:32.419 415M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 0 gaps after checking 24 candidates 0:01:32.436 415M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:01:32.436 415M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:01:32.436 415M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:01:32.437 415M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:01:32.437 415M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:32.437 415M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:32.457 415M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:32.457 415M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:32.473 415M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:32.474 415M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:32.491 415M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:32.491 415M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:32.507 415M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:32.507 415M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:01:32.561 415M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:01:34.331 401M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 66238 times 0:01:34.331 401M / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 4 and less 0:01:34.336 401M / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:01:34.340 401M / 7G INFO General (simplification.cpp : 502) Average coverage = 113.128 0:01:34.340 401M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:34.341 401M / 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/FAM24235-i1-2/1_spades_assembly/K77/simplified_contigs 0:01:34.371 405M / 7G INFO General (binary_converter.cpp : 111) 484 reads written 0:01:34.406 405M / 7G INFO General (launch.hpp : 192) SPAdes finished 0:01:34.491 250M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 1 minutes 34 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/FAM24235-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/FAM24235-i1-2/1_spades_assembly/K99/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/FAM24235-i1-2/1_spades_assembly/K99/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/FAM24235-i1-2/1_spades_assembly/K99/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/FAM24235-i1-2/1_spades_assembly/dataset.info) with K=99 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 0:00:00.005 5M / 14M INFO General (read_converter.cpp : 53) Binary reads detected 0:00:00.006 6M / 16M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction 0:00:00.006 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/FAM24235-i1-2/1_spades_assembly/K77/simplified_contigs 0:00:00.107 6M / 16M INFO General (construction.cpp : 150) Max read length 151 0:00:00.107 6M / 16M INFO General (construction.cpp : 156) Average read length 132.811 0:00:00.107 6M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.108 6M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:00.109 6M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.109 6M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933302 Gb 0:00:00.109 6M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 167772 0:00:06.629 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 8138458 reads 0:00:17.579 6G / 7G INFO General (kmer_splitters.hpp : 287) Processed 11152192 reads 0:00:17.719 115M / 7G INFO General (kmer_splitters.hpp : 293) Used 11152192 reads 0:00:17.719 115M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:25.144 115M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 15382001 kmers in total. 0:00:25.145 115M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:32.615 24M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:32.616 24M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:32.616 24M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:32.618 24M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:32.618 24M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933271 Gb 0:00:32.618 24M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:00:35.277 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 15382001 kmers 0:00:35.278 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 15382001 kmers. 0:00:35.467 81M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:36.219 81M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 15554503 kmers in total. 0:00:36.219 81M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:38.699 81M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:40.893 86M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:45.184 86M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 7223362 bytes occupied (3.71512 bits per kmer). 0:00:45.202 102M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:46.097 102M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:46.098 101M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:46.107 101M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:50.896 147M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 677056 sequences extracted 0:00:51.791 147M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:52.135 147M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:53.268 301M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:53.268 301M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:53.269 301M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:53.765 301M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 7137704 bytes occupied (3.71224 bits per kmer). 0:00:53.797 365M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:01:00.357 361M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:01:01.428 361M / 7G INFO General (construction.cpp : 505) Processed 1354111 edges 0:01:01.546 281M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:01:01.547 281M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 10 0:01:01.547 281M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 67 0:01:01.548 281M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 70. Coverage mad: 19.2738 0:01:01.548 281M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:01.644 281M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:01.926 281M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:02.965 281M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:05.397 281M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:05.608 281M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 70.9625. Fitted coverage std. dev: 17.1725 0:01:05.612 281M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.0191317 0:01:05.612 281M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 10 0:01:05.612 281M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 10 0:01:05.612 281M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2807476 0:01:05.613 281M / 7G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 70.9625 0:01:05.613 281M / 7G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 10 0:01:05.613 281M / 7G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 3 0:01:05.613 281M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:01:05.614 281M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:01:05.615 281M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:05.615 281M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:01:05.618 281M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:05.619 281M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.926301 Gb 0:01:05.619 281M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:01:07.731 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 1354111 edges 0:01:07.731 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 1354111 sequences. 0:01:07.814 299M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:10.418 299M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 15382001 kmers in total. 0:01:10.419 299M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:22.213 299M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:23.749 294M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:26.604 294M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 7140864 bytes occupied (3.71388 bits per kmer). 0:01:26.716 550M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:01:27.421 550M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:01:28.345 550M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:01:29.693 637M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:34.406 597M / 7G INFO General (gap_closer.cpp : 126) Used 2787806 paired reads 0:01:34.407 597M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:34.635 576M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:35.407 588M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 15 gaps after checking 325 candidates 0:01:35.477 587M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:01:35.488 331M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:01:35.489 331M / 7G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled 0:01:35.489 331M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:01:35.555 331M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:01:35.555 331M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:01:35.556 331M / 7G INFO General (simplification.cpp : 383) Graph simplification started 0:01:35.556 331M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:35.556 331M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:01:35.556 331M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.475 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 259195 times 0:01:38.475 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.530 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 56 times 0:01:38.531 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.567 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 44 times 0:01:38.568 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:01:38.568 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.570 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 32 times 0:01:38.570 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.572 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 0:01:38.573 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.575 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 30 times 0:01:38.575 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:01:38.576 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.576 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:01:38.576 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.577 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times 0:01:38.578 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.580 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 21 times 0:01:38.580 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:01:38.580 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.581 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:01:38.581 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.581 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:01:38.582 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.583 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9 times 0:01:38.583 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:01:38.583 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.583 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:38.584 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.584 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:38.584 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.585 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times 0:01:38.585 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:01:38.585 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.585 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:38.586 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.586 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:38.586 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.587 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times 0:01:38.587 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:01:38.587 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.587 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:38.588 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.588 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:38.588 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.588 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:38.588 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:01:38.589 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.589 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:38.589 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.589 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:38.590 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.590 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times 0:01:38.591 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:01:38.591 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.591 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:38.591 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.592 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:38.592 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.593 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times 0:01:38.593 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:01:38.593 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.593 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:38.594 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.594 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:38.594 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.594 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:38.595 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:01:38.595 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.641 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20 times 0:01:38.642 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.677 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:38.677 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.712 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:38.713 273M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:01:38.713 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:38.713 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:38.714 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:38.714 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:38.714 273M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:01:38.714 273M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:01:38.743 273M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:01:38.744 273M / 7G INFO General (graph_pack.hpp : 105) Index refill 0:01:38.746 273M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:38.746 273M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:01:38.748 273M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:01:38.749 273M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.925813 Gb 0:01:38.749 273M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:01:40.585 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 346413 edges 0:01:40.585 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 346413 sequences. 0:01:40.650 299M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:41.753 298M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 9627823 kmers in total. 0:01:41.753 298M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:44.275 298M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:45.251 281M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:47.475 281M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4472592 bytes occupied (3.71639 bits per kmer). 0:01:47.544 441M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:01:47.982 441M / 7G INFO General (edge_index.hpp : 92) Index refilled 0:01:48.041 441M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:01:48.635 484M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:52.472 465M / 7G INFO General (gap_closer.cpp : 126) Used 2787806 paired reads 0:01:52.472 465M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:52.587 453M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:52.835 453M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 0 gaps after checking 74 candidates 0:01:53.018 453M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:01:53.019 453M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:01:53.019 453M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:01:53.020 453M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:01:53.020 453M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:53.021 453M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.079 453M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:53.080 453M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.121 453M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:53.121 453M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:53.165 453M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:53.166 453M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:53.201 453M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:53.202 453M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:01:53.388 452M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:01:58.701 373M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 172809 times 0:01:58.702 373M / 7G INFO General (simplification.cpp : 353) Removing all the edges having coverage 3 and less 0:01:58.706 373M / 7G INFO General (simplification.cpp : 496) Counting average coverage 0:01:58.710 373M / 7G INFO General (simplification.cpp : 502) Average coverage = 76.1309 0:01:58.710 373M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:58.711 373M / 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/FAM24235-i1-2/1_spades_assembly/K99/simplified_contigs 0:01:58.723 377M / 7G INFO General (binary_converter.cpp : 111) 396 reads written 0:01:58.725 377M / 7G INFO General (launch.hpp : 192) SPAdes finished 0:01:58.737 168M / 7G INFO General (main.cpp : 105) Assembling time: 0 hours 1 minutes 58 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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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 0:00:00.005 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/FAM24235-i1-2/1_spades_assembly/K99/simplified_contigs 0:00:00.053 6M / 16M INFO General (construction.cpp : 150) Max read length 151 0:00:00.053 6M / 16M INFO General (construction.cpp : 156) Average read length 132.811 0:00:00.053 6M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting 0:00:00.054 6M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 100 files using 10 threads. This might take a while. 0:00:00.054 6M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:00.054 6M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933302 Gb 0:00:00.054 6M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 167772 0:00:05.613 6G / 6G INFO General (kmer_splitters.hpp : 287) Processed 11152016 reads 0:00:05.702 132M / 5G INFO General (kmer_splitters.hpp : 293) Used 11152016 reads 0:00:05.702 132M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:06.317 126M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 9088586 kmers in total. 0:00:06.318 126M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:08.381 108M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction 0:00:08.382 108M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:08.382 108M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:08.383 108M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:08.384 108M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.933271 Gb 0:00:08.384 108M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:00:10.787 7G / 7G INFO General (kmer_splitters.hpp : 364) Processed 9088586 kmers 0:00:10.787 7G / 7G INFO General (kmer_splitters.hpp : 369) Used 9088586 kmers. 0:00:10.978 95M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:15.161 95M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 9340005 kmers in total. 0:00:15.162 95M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:26.005 95M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:28.197 71M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:28.845 71M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4339128 bytes occupied (3.7166 bits per kmer). 0:00:28.853 81M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:30.563 81M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:30.564 81M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph 0:00:30.581 81M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:32.731 101M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 488976 sequences extracted 0:00:33.301 101M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:33.553 101M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:34.366 215M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) 0:00:34.367 215M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:34.367 215M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:34.650 218M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4219520 bytes occupied (3.71413 bits per kmer). 0:00:34.661 258M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. 0:00:38.404 257M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM 0:00:38.943 257M / 5G INFO General (construction.cpp : 505) Processed 977952 edges 0:00:39.026 207M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding 0:00:39.026 207M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 3 0:00:39.027 207M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 27 0:00:39.027 207M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 30. Coverage mad: 10.3782 0:00:39.027 207M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:39.075 207M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:39.184 207M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:39.526 207M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:40.284 207M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:00:41.484 207M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 30.3086. Fitted coverage std. dev: 8.74734 0:00:41.485 207M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.985394 0:00:41.486 207M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 16 0:00:41.486 207M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 16 0:00:41.486 207M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2709462 0:00:41.486 207M / 5G INFO General (genomic_info_filler.cpp : 120) Mean coverage was calculated as 30.3086 0:00:41.486 207M / 5G INFO General (genomic_info_filler.cpp : 135) EC coverage threshold value was calculated as 16 0:00:41.487 207M / 5G INFO General (genomic_info_filler.cpp : 136) Trusted kmer low bound: 1 0:00:41.487 207M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:00:41.487 207M / 5G INFO General (graph_pack.hpp : 105) Index refill 0:00:41.488 207M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:41.488 207M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:41.489 206M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:41.490 206M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.928067 Gb 0:00:41.490 206M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:00:43.792 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 977952 edges 0:00:43.793 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 977952 sequences. 0:00:43.915 245M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:45.415 240M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 9088586 kmers in total. 0:00:45.416 240M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:48.055 240M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:49.900 227M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:50.976 227M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4222632 bytes occupied (3.71687 bits per kmer). 0:00:51.040 387M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:51.482 383M / 5G INFO General (edge_index.hpp : 92) Index refilled 0:00:52.544 383M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:00:53.608 468M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:00:55.643 452M / 5G INFO General (gap_closer.cpp : 126) Used 2787806 paired reads 0:00:55.644 452M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices 0:00:55.848 423M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:00:56.428 431M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 13 gaps after checking 209 candidates 0:00:56.461 430M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification 0:00:56.465 270M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:56.465 270M / 5G INFO General (simplification.cpp : 63) Most init cleaning disabled on main iteration 0:00:56.466 270M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:56.507 270M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:56.508 270M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification 0:00:56.508 270M / 5G INFO General (simplification.cpp : 383) Graph simplification started 0:00:56.508 270M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:00:56.508 270M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 0:00:56.509 270M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.657 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 120446 times 0:00:57.657 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.701 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 17 times 0:00:57.702 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.739 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times 0:00:57.739 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 0:00:57.739 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.740 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:00:57.740 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.740 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.740 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.742 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times 0:00:57.742 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 0:00:57.742 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.743 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:57.743 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.743 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.743 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.744 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times 0:00:57.744 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 0:00:57.745 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.745 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:57.745 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.745 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.745 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.746 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:57.746 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 0:00:57.746 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.746 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:57.747 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.747 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.747 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.747 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:57.747 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 0:00:57.748 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.748 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:57.748 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.748 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.748 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.749 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:00:57.749 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 0:00:57.749 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.749 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:57.750 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.750 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.750 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.750 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:57.750 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 0:00:57.751 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.751 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:57.751 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.751 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.752 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.752 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times 0:00:57.752 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 0:00:57.752 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.753 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:57.753 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.753 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.753 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.754 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:00:57.754 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 0:00:57.754 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.754 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:57.754 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.755 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.755 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.755 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times 0:00:57.755 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 0:00:57.755 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.802 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:00:57.802 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.838 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.839 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.874 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:57.874 224M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 0:00:57.875 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:57.875 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:57.875 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:57.875 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:57.876 224M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:57.876 224M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:57.899 224M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer 0:00:57.900 224M / 5G INFO General (graph_pack.hpp : 105) Index refill 0:00:57.919 224M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:57.919 224M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 160 files using 10 threads. This might take a while. 0:00:57.921 224M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 131072 0:00:57.922 224M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.927698 Gb 0:00:57.922 224M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:01:00.361 7G / 7G INFO General (edge_index_builders.hpp : 77) Processed 503782 edges 0:01:00.362 7G / 7G INFO General (edge_index_builders.hpp : 82) Used 503782 sequences. 0:01:00.411 264M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:01.849 257M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7896900 kmers in total. 0:01:01.849 257M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:03.055 257M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:03.851 231M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:06.557 231M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3670080 bytes occupied (3.718 bits per kmer). 0:01:06.620 359M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:01:07.020 353M / 5G INFO General (edge_index.hpp : 92) Index refilled 0:01:07.124 353M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps 0:01:07.785 411M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) 0:01:10.860 395M / 5G INFO General (gap_closer.cpp : 126) Used 2787806 paired reads 0:01:10.861 395M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices 0:01:11.044 384M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps 0:01:11.399 383M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 1 gaps after checking 141 candidates 0:01:11.428 383M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup 0:01:11.428 383M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:01:11.428 383M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled 0:01:11.429 383M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled 0:01:11.429 383M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance 0:01:11.429 383M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.476 383M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:11.476 383M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.514 383M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.514 383M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:01:11.562 383M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:01:11.563 383M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:01:11.599 383M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:01:11.599 383M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges 0:01:11.808 383M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:01:16.257 307M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 251562 times 0:01:16.257 307M / 5G INFO General (simplification.cpp : 353) Removing all the edges having coverage 1 and less 0:01:16.260 307M / 5G INFO General (simplification.cpp : 496) Counting average coverage 0:01:16.263 307M / 5G INFO General (simplification.cpp : 502) Average coverage = 32.3679 0:01:16.263 307M / 5G INFO StageManager (stage.cpp : 166) STAGE == Mismatch Correction 0:01:16.264 307M / 5G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 4896 kmers to process 0:01:16.266 307M / 5G INFO General (graph_pack.hpp : 115) Normalizing done 0:01:20.775 268M / 5G INFO General (mismatch_shall_not_pass.hp: 195) Finished collecting potential mismatches positions 0:01:20.782 268M / 5G INFO General (mismatch_shall_not_pass.hp: 303) All edges processed 0:01:20.784 261M / 5G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides 0:01:20.814 261M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:20.814 261M / 5G 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/FAM24235-i1-2/1_spades_assembly/K127/assembly_graph_with_scaffolds.gfa 0:01:21.122 262M / 5G 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/FAM24235-i1-2/1_spades_assembly/K127/before_rr.fasta 0:01:21.304 262M / 5G 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/FAM24235-i1-2/1_spades_assembly/K127/assembly_graph.fastg 0:01:21.509 262M / 5G 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/FAM24235-i1-2/1_spades_assembly/K127/final_contigs.fasta 0:01:21.561 261M / 5G INFO StageManager (stage.cpp : 166) STAGE == Paired Information Counting 0:01:21.568 261M / 5G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 4896 kmers to process 0:01:21.568 261M / 5G INFO General (graph_pack.hpp : 115) Normalizing done 0:01:21.571 261M / 5G INFO General (pair_info_count.cpp : 322) Min edge length for estimation: 50625 0:01:21.572 261M / 5G INFO General (pair_info_count.cpp : 333) Estimating insert size for library #0 0:01:21.572 261M / 5G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:01:21.672 437M / 5G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:01:22.781 394M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 200000 reads 0:01:22.806 394M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 400000 reads 0:01:22.830 394M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 600000 reads 0:01:22.856 394M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 800000 reads 0:01:22.931 393M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 1000000 reads 0:01:22.956 392M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 1200000 reads 0:01:25.129 381M / 5G INFO General (sequence_mapper_notifier.h: 94) Total 2787806 reads processed 0:01:25.427 381M / 5G INFO General (pair_info_count.cpp : 208) Edge pairs: 5280 0:01:25.428 381M / 5G INFO General (pair_info_count.cpp : 212) 785716 paired reads (28.184% of all) aligned to long edges 0:01:25.519 204M / 5G INFO General (pair_info_count.cpp : 356) Insert size = 437.682, deviation = 101.676, left quantile = 317, right quantile = 570, read length = 151 0:01:25.520 204M / 5G INFO General (pair_info_count.cpp : 373) Filtering data for library #0 0:01:25.577 204M / 5G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:01:26.552 203M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 200000 reads 0:01:26.711 202M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 400000 reads 0:01:26.764 202M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 600000 reads 0:01:26.802 202M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 800000 reads 0:01:26.805 202M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 1000000 reads 0:01:26.811 202M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 1200000 reads 0:01:27.571 202M / 5G INFO General (sequence_mapper_notifier.h: 94) Total 2787806 reads processed 0:01:27.572 202M / 5G INFO General (pair_info_count.cpp : 385) Mapping library #0 0:01:27.573 202M / 5G INFO General (pair_info_count.cpp : 387) Mapping paired reads (takes a while) 0:01:27.573 202M / 5G INFO General (pair_info_count.cpp : 288) Left insert size quantile 317, right insert size quantile 570, filtering threshold 2, rounding threshold 0 0:01:27.592 211M / 5G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:01:28.759 212M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 200000 reads 0:01:28.781 212M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 400000 reads 0:01:28.834 213M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 600000 reads 0:01:28.860 213M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 800000 reads 0:01:28.888 213M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 1000000 reads 0:01:28.934 213M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 1200000 reads 0:01:29.265 213M / 5G INFO General (sequence_mapper_notifier.h: 76) Processed 2157600 reads 0:01:30.390 213M / 5G INFO General (sequence_mapper_notifier.h: 94) Total 2787806 reads processed 0:01:30.878 213M / 5G INFO StageManager (stage.cpp : 166) STAGE == Distance Estimation 0:01:30.879 213M / 5G INFO General (distance_estimation.cpp : 174) Processing library #0 0:01:30.879 213M / 5G INFO General (distance_estimation.cpp : 150) Weight Filter Done 0:01:30.880 213M / 5G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:01:30.890 209M / 5G INFO General (distance_estimation.cpp : 35) Filtering info 0:01:30.890 209M / 5G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2890 0:01:30.893 209M / 5G INFO General (pair_info_filters.hpp : 263) Done filtering 0:01:30.893 209M / 5G INFO General (distance_estimation.cpp : 157) Refining clustered pair information 0:01:30.895 209M / 5G INFO General (distance_estimation.cpp : 159) The refining of clustered pair information has been finished 0:01:30.895 209M / 5G INFO General (distance_estimation.cpp : 161) Improving paired information 0:01:30.911 209M / 5G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 123; contradictional = 58 0:01:30.925 209M / 5G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 9; contradictional = 16 0:01:30.925 209M / 5G INFO General (distance_estimation.cpp : 104) Filling scaffolding index 0:01:30.926 209M / 5G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:01:30.936 210M / 5G INFO General (distance_estimation.cpp : 35) Filtering info 0:01:30.937 210M / 5G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 786 0:01:30.937 210M / 5G INFO General (pair_info_filters.hpp : 263) Done filtering 0:01:30.938 210M / 5G INFO General (distance_estimation.cpp : 183) Clearing raw paired index 0:01:30.939 210M / 5G INFO StageManager (stage.cpp : 166) STAGE == Repeat Resolving 0:01:30.939 210M / 5G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:01:30.939 210M / 5G INFO General (launcher.cpp : 538) ExSPAnder repeat resolving tool started 0:01:30.949 211M / 5G INFO General (launcher.cpp : 404) Creating main extenders, unique edge length = 2000 0:01:30.950 211M / 5G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 32.3679 0:01:30.953 211M / 5G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 32.3679 0:01:30.963 211M / 5G INFO General (extenders_logic.cpp : 519) Using 1 paired-end library 0:01:30.963 211M / 5G INFO General (extenders_logic.cpp : 520) Using 1 paired-end scaffolding library 0:01:30.964 211M / 5G INFO General (extenders_logic.cpp : 521) Using 0 single read libraries 0:01:30.964 211M / 5G INFO General (launcher.cpp : 432) Total number of extenders is 3 0:01:30.964 211M / 5G INFO General (path_extender.hpp : 894) Processed 0 paths from 324 (0%) 0:01:31.021 212M / 5G INFO General (path_extender.hpp : 894) Processed 33 paths from 324 (10%) 0:01:31.075 212M / 5G INFO General (path_extender.hpp : 894) Processed 66 paths from 324 (20%) 0:01:31.099 213M / 5G INFO General (path_extender.hpp : 894) Processed 99 paths from 324 (30%) 0:01:31.103 213M / 5G INFO General (path_extender.hpp : 892) Processed 128 paths from 324 (39%) 0:01:31.103 213M / 5G INFO General (path_extender.hpp : 894) Processed 132 paths from 324 (40%) 0:01:31.105 213M / 5G INFO General (path_extender.hpp : 894) Processed 165 paths from 324 (50%) 0:01:31.108 213M / 5G INFO General (path_extender.hpp : 894) Processed 198 paths from 324 (61%) 0:01:31.109 213M / 5G INFO General (path_extender.hpp : 894) Processed 231 paths from 324 (71%) 0:01:31.109 213M / 5G INFO General (path_extender.hpp : 892) Processed 256 paths from 324 (79%) 0:01:31.109 213M / 5G INFO General (path_extender.hpp : 894) Processed 264 paths from 324 (81%) 0:01:31.110 213M / 5G INFO General (path_extender.hpp : 894) Processed 297 paths from 324 (91%) 0:01:31.110 213M / 5G INFO General (launcher.cpp : 244) Finalizing paths 0:01:31.110 213M / 5G INFO General (launcher.cpp : 246) Deduplicating paths 0:01:31.112 213M / 5G INFO General (launcher.cpp : 250) Paths deduplicated 0:01:31.112 213M / 5G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:01:31.113 213M / 5G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:01:31.113 213M / 5G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:01:31.113 213M / 5G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:01:31.117 213M / 5G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:01:31.120 213M / 5G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:01:31.122 213M / 5G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:01:31.123 213M / 5G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:01:31.127 213M / 5G INFO General (launcher.cpp : 267) Paths finalized 0:01:31.127 213M / 5G INFO General (launcher.cpp : 439) Closing gaps in paths 0:01:31.128 213M / 5G INFO General (launcher.cpp : 467) Gap closing completed 0:01:31.131 213M / 5G INFO General (launcher.cpp : 296) Traversing tandem repeats 0:01:31.136 213M / 5G INFO General (launcher.cpp : 306) Traversed 1 loops 0:01:31.136 213M / 5G INFO General (launcher.cpp : 244) Finalizing paths 0:01:31.136 213M / 5G INFO General (launcher.cpp : 246) Deduplicating paths 0:01:31.137 213M / 5G INFO General (launcher.cpp : 250) Paths deduplicated 0:01:31.137 213M / 5G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:01:31.137 213M / 5G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:01:31.137 213M / 5G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:01:31.138 213M / 5G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:01:31.138 213M / 5G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:01:31.139 213M / 5G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:01:31.139 213M / 5G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:01:31.140 213M / 5G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:01:31.143 213M / 5G INFO General (launcher.cpp : 267) Paths finalized 0:01:31.143 213M / 5G INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished 0:01:31.145 213M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output 0:01:31.145 213M / 5G 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/FAM24235-i1-2/1_spades_assembly/K127/assembly_graph_with_scaffolds.gfa 0:01:31.463 214M / 5G 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/FAM24235-i1-2/1_spades_assembly/K127/before_rr.fasta 0:01:31.843 214M / 5G 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/FAM24235-i1-2/1_spades_assembly/K127/assembly_graph.fastg 0:01:32.239 214M / 5G 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/FAM24235-i1-2/1_spades_assembly/K127/final_contigs.paths 0:01:32.421 216M / 5G 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/FAM24235-i1-2/1_spades_assembly/K127/scaffolds.paths 0:01:32.546 216M / 5G INFO General (launch.hpp : 192) SPAdes finished 0:01:32.556 56M / 5G INFO General (main.cpp : 105) Assembling time: 0 hours 1 minutes 32 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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-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/FAM24235-i1-2/1_spades_assembly/spades.log Thank you for using SPAdes!