Command line: /home/deren/miniconda3/bin/spades.py -o /home/deren/Documents/genomics-course/session-11/notebooks/test-1 -1 /home/deren/Documents/genomics-course/session-11/notebooks/SRR7825135_1.trim.fastq -2 /home/deren/Documents/genomics-course/session-11/notebooks/SRR7825135_2.trim.fastq -m 64 -t 20 System information: SPAdes version: 3.13.0 Python version: 3.6.8 OS: Linux-4.4.0-141-generic-x86_64-with-debian-stretch-sid Output dir: /home/deren/Documents/genomics-course/session-11/notebooks/test-1 Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/home/deren/Documents/genomics-course/session-11/notebooks/SRR7825135_1.trim.fastq'] right reads: ['/home/deren/Documents/genomics-course/session-11/notebooks/SRR7825135_2.trim.fastq'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /home/deren/Documents/genomics-course/session-11/notebooks/test-1/tmp Threads: 20 Memory limit (in Gb): 64 ======= SPAdes pipeline started. Log can be found here: /home/deren/Documents/genomics-course/session-11/notebooks/test-1/spades.log ===== Read error correction started. == Running read error correction tool: /home/deren/miniconda3/share/spades-3.13.0-0/bin/spades-hammer /home/deren/Documents/genomics-course/session-11/notebooks/test-1/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /home/deren/Documents/genomics-course/session-11/notebooks/test-1/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 20 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 64 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.000 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.001 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.001 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.001 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 320 files using 20 threads. This might take a while. 0:00:00.001 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.0666 Gb 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:00:00.040 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /home/deren/Documents/genomics-course/session-11/notebooks/SRR7825135_1.trim.fastq 0:01:03.142 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 7473712 reads 0:01:42.426 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 11024477 reads 0:01:42.427 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /home/deren/Documents/genomics-course/session-11/notebooks/SRR7825135_2.trim.fastq 0:02:57.398 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 18940136 reads 0:03:23.551 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 22048954 reads 0:03:23.551 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 112) Total 22048954 reads processed 0:03:24.880 80M / 11G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:03:32.627 80M / 11G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 129234734 kmers in total. 0:03:32.627 80M / 11G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:03:34.024 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:03:41.752 144M / 11G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:03:51.548 144M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 59934584 bytes occupied (3.71012 bits per kmer). 0:03:52.263 144M / 11G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:04:00.641 2G / 11G INFO General (main.cpp : 148) Clustering Hamming graph. 0:09:56.677 2G / 11G INFO General (main.cpp : 155) Extracting clusters 0:11:17.529 2G / 11G INFO General (main.cpp : 167) Clustering done. Total clusters: 46934679 0:11:17.631 1G / 11G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 0:11:19.797 3G / 11G INFO K-mer Counting (kmer_data.cpp : 382) Processing /home/deren/Documents/genomics-course/session-11/notebooks/SRR7825135_1.trim.fastq 0:15:16.357 3G / 11G INFO K-mer Counting (kmer_data.cpp : 382) Processing /home/deren/Documents/genomics-course/session-11/notebooks/SRR7825135_2.trim.fastq 0:19:21.911 3G / 11G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 0:19:22.595 3G / 11G INFO K-mer Counting (kmer_data.cpp : 403) There are 129234734 kmers in total. Among them 82198988 (63.6044%) are singletons. 0:19:22.596 3G / 11G INFO General (main.cpp : 173) Subclustering Hamming graph 0:20:50.274 3G / 11G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 721 non-read kmers were generated. 0:20:50.274 3G / 11G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 0:20:50.275 3G / 11G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 17118088. Among them 9163452 (53.5308%) are good 0:20:50.275 3G / 11G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 1264676. Among them 1259414 (99.5839%) are good 0:20:50.275 3G / 11G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 31686639. Among them 20823274 (65.7163%) are good 0:20:50.275 3G / 11G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 3.53832 kmers 0:20:50.276 3G / 11G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.10513 0:20:50.276 3G / 11G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 31246140 0:20:50.276 3G / 11G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.953134,0.0206491,0.0146581,0.0115587),(0.0293213,0.946009,0.00939293,0.015277),(0.015217,0.00937467,0.946069,0.0293396),(0.0115416,0.0146245,0.0206306,0.953203)) 0:20:50.403 3G / 11G INFO General (main.cpp : 178) Finished clustering. 0:20:50.404 3G / 11G INFO General (main.cpp : 197) Starting solid k-mers expansion in 20 threads. 0:24:22.374 3G / 11G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 1197335 new k-mers. 0:28:16.078 3G / 11G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 46325 new k-mers. 0:31:38.367 3G / 11G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 1739 new k-mers. 0:35:03.117 3G / 11G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 92 new k-mers. 0:38:47.705 3G / 11G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 0 new k-mers. 0:38:47.705 3G / 11G INFO General (main.cpp : 222) Solid k-mers finalized 0:38:47.705 3G / 11G INFO General (hammer_tools.cpp : 220) Starting read correction in 20 threads. 0:38:47.705 3G / 11G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /home/deren/Documents/genomics-course/session-11/notebooks/SRR7825135_1.trim.fastq and /home/deren/Documents/genomics-course/session-11/notebooks/SRR7825135_2.trim.fastq 0:39:00.633 5G / 11G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2000000 reads. 0:39:19.080 6G / 11G INFO General (hammer_tools.cpp : 175) Processed batch 0 0:39:25.402 6G / 11G INFO General (hammer_tools.cpp : 185) Written batch 0 0:39:37.533 6G / 11G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 2000000 reads. 0:39:54.535 6G / 11G INFO General (hammer_tools.cpp : 175) Processed batch 1 0:40:01.008 6G / 11G INFO General (hammer_tools.cpp : 185) Written batch 1 0:40:12.587 6G / 11G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 2000000 reads. 0:40:32.768 6G / 11G INFO General (hammer_tools.cpp : 175) Processed batch 2 0:40:43.450 6G / 11G INFO General (hammer_tools.cpp : 185) Written batch 2 0:40:55.277 6G / 11G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 2000000 reads. 0:41:12.956 6G / 11G INFO General (hammer_tools.cpp : 175) Processed batch 3 0:41:25.135 6G / 11G INFO General (hammer_tools.cpp : 185) Written batch 3 0:41:37.551 6G / 11G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 2000000 reads. 0:41:55.662 6G / 11G INFO General (hammer_tools.cpp : 175) Processed batch 4 0:42:05.076 6G / 11G INFO General (hammer_tools.cpp : 185) Written batch 4 0:42:11.483 6G / 11G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 1024477 reads. 0:42:20.559 6G / 11G INFO General (hammer_tools.cpp : 175) Processed batch 5 0:42:24.109 6G / 11G INFO General (hammer_tools.cpp : 185) Written batch 5 0:42:27.322 3G / 11G INFO General (hammer_tools.cpp : 274) Correction done. Changed 3033073 bases in 2440874 reads. 0:42:27.323 3G / 11G INFO General (hammer_tools.cpp : 275) Failed to correct 240733 bases out of 2120857081. 0:42:27.718 80M / 11G INFO General (main.cpp : 255) Saving corrected dataset description to /home/deren/Documents/genomics-course/session-11/notebooks/test-1/corrected/corrected.yaml 0:42:27.719 80M / 11G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with pigz) == Dataset description file was created: /home/deren/Documents/genomics-course/session-11/notebooks/test-1/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /home/deren/Documents/genomics-course/session-11/notebooks/test-1/K21/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 64 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/home/deren/Documents/genomics-course/session-11/notebooks/test-1/dataset.info) with K=21 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 20 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.346 80M / 80M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:00:00.604 92M / 92M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:00:01.280 112M / 112M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:00:02.387 160M / 160M INFO General (binary_converter.hpp : 93) 131072 reads processed 0:00:04.442 252M / 252M INFO General (binary_converter.hpp : 93) 262144 reads processed 0:00:08.577 436M / 436M INFO General (binary_converter.hpp : 93) 524288 reads processed 0:00:20.517 728M / 728M INFO General (binary_converter.hpp : 93) 1048576 reads processed 0:00:40.999 736M / 736M INFO General (binary_converter.hpp : 93) 2097152 reads processed 0:01:20.463 748M / 748M INFO General (binary_converter.hpp : 93) 4194304 reads processed 0:02:47.681 760M / 760M INFO General (binary_converter.hpp : 93) 8388608 reads processed 0:03:38.181 708M / 760M INFO General (binary_converter.hpp : 117) 10942735 reads written 0:03:39.461 4M / 760M INFO General (read_converter.hpp : 87) Converting single reads 0:03:39.738 168M / 760M INFO General (binary_converter.hpp : 93) 16384 reads processed 0:03:39.857 176M / 760M INFO General (binary_converter.hpp : 93) 32768 reads processed 0:03:40.096 184M / 760M INFO General (binary_converter.hpp : 93) 65536 reads processed 0:03:40.338 188M / 760M INFO General (binary_converter.hpp : 117) 79419 reads written 0:03:40.406 4M / 760M INFO General (read_converter.hpp : 95) Converting merged reads 0:03:40.581 164M / 760M INFO General (binary_converter.hpp : 117) 0 reads written 0:03:40.641 4M / 760M INFO General (construction.cpp : 111) Max read length 100 0:03:40.641 4M / 760M INFO General (construction.cpp : 117) Average read length 96.4783 0:03:40.641 4M / 760M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:03:40.641 4M / 760M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 400 files using 20 threads. This might take a while. 0:03:40.641 4M / 760M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:03:40.641 4M / 760M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.0666 Gb 0:03:40.641 4M / 760M INFO General (kmer_splitters.hpp : 97) Using cell size of 167772 0:04:14.991 11G / 11G INFO General (kmer_splitters.hpp : 289) Processed 34352110 reads 0:04:26.145 11G / 11G INFO General (kmer_splitters.hpp : 289) Processed 43929778 reads 0:04:26.145 11G / 11G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:04:27.539 80M / 11G INFO General (kmer_splitters.hpp : 308) Used 43929778 reads 0:04:27.540 80M / 11G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:04:30.597 80M / 11G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 23953931 kmers in total. 0:04:30.597 80M / 11G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:04:30.840 80M / 11G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:04:30.841 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:04:30.841 80M / 11G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 320 files using 20 threads. This might take a while. 0:04:30.842 80M / 11G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:04:30.842 80M / 11G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.06536 Gb 0:04:30.842 80M / 11G INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:04:34.770 11G / 11G INFO General (kmer_splitters.hpp : 380) Processed 23953931 kmers 0:04:34.770 11G / 11G INFO General (kmer_splitters.hpp : 385) Used 23953931 kmers. 0:04:34.922 80M / 11G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:04:36.038 80M / 11G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 23785725 kmers in total. 0:04:36.038 80M / 11G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:04:36.276 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:04:37.649 80M / 11G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:04:38.650 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 11037456 bytes occupied (3.7123 bits per kmer). 0:04:38.716 104M / 11G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:04:40.890 104M / 11G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:04:40.891 104M / 11G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:04:40.891 104M / 11G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:04:40.891 104M / 11G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:04:45.417 104M / 11G INFO Early tip clipping (early_simplification.hpp : 184) 1210838 22-mers were removed by early tip clipper 0:04:45.417 104M / 11G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:04:45.418 104M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:04:47.975 120M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 503314 sequences extracted 0:04:49.399 120M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:04:50.029 120M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 10 loops collected 0:04:50.480 228M / 11G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:04:50.480 228M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:04:50.480 228M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:04:51.677 256M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 11117672 bytes occupied (3.71302 bits per kmer). 0:04:51.755 348M / 11G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:05:47.134 344M / 11G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:05:48.945 344M / 11G INFO General (construction.cpp : 464) Processed 1005258 edges 0:05:49.081 200M / 11G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:05:49.084 200M / 11G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 9 0:05:49.084 200M / 11G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 54 0:05:49.084 200M / 11G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 57. Coverage mad: 14.826 0:05:49.085 200M / 11G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:05:49.205 200M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:05:49.548 200M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:05:50.849 200M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:05:53.511 200M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:05:55.181 196M / 11G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 57.9046. Fitted coverage std. dev: 15.3841 0:05:55.185 196M / 11G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.922082 0:05:55.185 196M / 11G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 27 0:05:55.185 196M / 11G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 27 0:05:55.185 196M / 11G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 19998426 0:05:55.186 196M / 11G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 57.9046 0:05:55.186 196M / 11G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 27 0:05:55.186 196M / 11G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:05:55.186 196M / 11G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:05:55.186 196M / 11G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:05:55.189 196M / 11G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:05:55.189 196M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:05:55.254 196M / 11G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:05:55.254 196M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:05:55.362 192M / 11G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 946 times 0:05:55.362 192M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:05:58.711 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 74525 times 0:05:58.711 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:05:58.817 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 8127 times 0:05:58.850 204M / 11G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:05:58.850 204M / 11G INFO General (simplification.cpp : 357) Graph simplification started 0:05:58.850 204M / 11G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:05:58.850 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:05:58.850 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:05:58.898 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 156 times 0:05:58.898 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:05.442 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 43590 times 0:06:05.442 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:05.652 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1898 times 0:06:05.653 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:06:05.653 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:05.684 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5 times 0:06:05.684 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:05.853 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 319 times 0:06:05.853 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:05.985 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2177 times 0:06:05.985 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:06:05.986 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:05.988 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:06:05.989 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:06.163 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 474 times 0:06:06.164 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:06.186 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 404 times 0:06:06.187 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:06:06.187 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:06.189 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:06.189 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:06.266 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 115 times 0:06:06.266 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:06.272 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 166 times 0:06:06.273 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:06:06.273 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:06.273 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:06.274 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:06.288 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 64 times 0:06:06.288 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:06.291 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 97 times 0:06:06.292 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:06:06.292 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:06.292 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:06.300 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:06.306 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 37 times 0:06:06.306 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:06.312 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 166 times 0:06:06.312 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:06:06.312 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:06.312 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:06.312 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:06.323 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 42 times 0:06:06.324 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:06.339 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 379 times 0:06:06.339 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:06:06.339 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:06.340 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:06.340 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:06.374 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 108 times 0:06:06.374 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:06.403 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 791 times 0:06:06.404 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:06:06.404 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:06.405 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:06.405 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:06.527 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 230 times 0:06:06.527 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:06.594 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1316 times 0:06:06.594 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:06:06.594 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:06.596 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:06.597 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:06.764 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 362 times 0:06:06.764 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:06.835 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1677 times 0:06:06.836 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:06:06.836 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:06.863 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:06.863 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:07.911 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 569 times 0:06:07.912 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:07.948 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:06:07.948 204M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:06:07.949 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:07.950 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:07.950 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:07.950 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:06:07.950 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:06:07.951 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:06:07.951 204M / 11G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:06:07.951 204M / 11G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:06:07.951 204M / 11G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:06:07.951 204M / 11G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:06:07.951 204M / 11G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:06:07.951 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:07.987 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:07.987 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:08.896 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:06:08.896 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:06:08.926 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:06:08.926 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:06:09.822 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:06:09.823 204M / 11G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:06:10.017 204M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:06:10.059 204M / 11G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 499 times 0:06:10.060 204M / 11G INFO General (simplification.cpp : 470) Counting average coverage 0:06:10.137 204M / 11G INFO General (simplification.cpp : 476) Average coverage = 84.1011 0:06:10.138 204M / 11G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:06:10.138 204M / 11G INFO General (contig_output_stage.cpp : 40) Writing GFA to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K21/assembly_graph_with_scaffolds.gfa 0:06:11.030 204M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K21/before_rr.fasta 0:06:12.177 204M / 11G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K21/assembly_graph.fastg 0:06:15.925 204M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K21/simplified_contigs.fasta 0:06:17.048 204M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K21/final_contigs.fasta 0:06:18.171 204M / 11G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:06:18.171 204M / 11G INFO General (contig_output_stage.cpp : 40) Writing GFA to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K21/assembly_graph_with_scaffolds.gfa 0:06:19.086 204M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K21/before_rr.fasta 0:06:20.262 204M / 11G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K21/assembly_graph.fastg 0:06:24.294 204M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K21/simplified_contigs.fasta 0:06:25.901 204M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K21/final_contigs.fasta 0:06:27.428 204M / 11G INFO General (launch.hpp : 149) SPAdes finished 0:06:27.936 80M / 11G INFO General (main.cpp : 109) Assembling time: 0 hours 6 minutes 27 seconds Max read length detected as 100 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /home/deren/Documents/genomics-course/session-11/notebooks/test-1/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 64 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/home/deren/Documents/genomics-course/session-11/notebooks/test-1/dataset.info) with K=33 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 20 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.001 4M / 4M INFO General (construction.cpp : 111) Max read length 100 0:00:00.001 4M / 4M INFO General (construction.cpp : 117) Average read length 96.4783 0:00:00.001 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 400 files using 20 threads. This might take a while. 0:00:00.001 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.0666 Gb 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 83886 0:00:23.052 11G / 11G INFO General (kmer_splitters.hpp : 289) Processed 20613133 reads 0:00:44.252 11G / 11G INFO General (kmer_splitters.hpp : 289) Processed 41037749 reads 0:00:49.677 11G / 11G INFO General (kmer_splitters.hpp : 289) Processed 43929778 reads 0:00:49.677 11G / 11G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:58.454 80M / 11G INFO General (kmer_splitters.hpp : 308) Used 43929778 reads 0:00:58.454 80M / 11G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:01.506 80M / 11G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 25488138 kmers in total. 0:01:01.506 80M / 11G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:02.021 80M / 11G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:01:02.021 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:02.021 80M / 11G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 320 files using 20 threads. This might take a while. 0:01:02.022 80M / 11G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:01:02.022 80M / 11G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.06536 Gb 0:01:02.022 80M / 11G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:01:06.566 11G / 11G INFO General (kmer_splitters.hpp : 380) Processed 25488138 kmers 0:01:06.567 11G / 11G INFO General (kmer_splitters.hpp : 385) Used 25488138 kmers. 0:01:06.773 80M / 11G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:08.404 80M / 11G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 25383359 kmers in total. 0:01:08.404 80M / 11G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:08.898 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:10.362 80M / 11G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:13.107 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 11778472 bytes occupied (3.71219 bits per kmer). 0:01:13.161 108M / 11G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:01:15.590 108M / 11G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:01:15.591 108M / 11G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:01:15.591 108M / 11G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:01:15.591 108M / 11G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:01:20.488 108M / 11G INFO Early tip clipping (early_simplification.hpp : 184) 1997986 34-mers were removed by early tip clipper 0:01:20.488 108M / 11G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:01:20.489 108M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:01:22.926 120M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 352927 sequences extracted 0:01:24.573 120M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:01:25.306 120M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 13 loops collected 0:01:25.718 192M / 11G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:01:25.718 192M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:25.718 192M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:26.982 220M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 11828976 bytes occupied (3.71278 bits per kmer). 0:01:27.084 320M / 11G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:02:15.406 320M / 11G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:02:17.282 320M / 11G INFO General (construction.cpp : 464) Processed 704706 edges 0:02:17.494 144M / 11G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:02:17.496 144M / 11G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7 0:02:17.496 144M / 11G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 45 0:02:17.496 144M / 11G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 47. Coverage mad: 13.3434 0:02:17.497 144M / 11G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:02:17.621 144M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:02:17.927 144M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:02:18.925 144M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:02:20.958 144M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:02:21.468 144M / 11G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 47.8719. Fitted coverage std. dev: 14.0448 0:02:21.472 144M / 11G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.745938 0:02:21.472 144M / 11G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 20 0:02:21.472 144M / 11G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 20 0:02:21.472 144M / 11G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 21016917 0:02:21.473 144M / 11G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 47.8719 0:02:21.473 144M / 11G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 20 0:02:21.473 144M / 11G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:02:21.473 144M / 11G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:02:21.473 144M / 11G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:02:21.474 144M / 11G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:02:21.474 144M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:02:21.544 144M / 11G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:02:21.544 144M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:02:21.644 144M / 11G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 1674 times 0:02:21.644 144M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:02:23.837 152M / 11G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 41460 times 0:02:23.837 152M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:02:23.951 152M / 11G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 11728 times 0:02:23.980 152M / 11G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:02:23.980 152M / 11G INFO General (simplification.cpp : 357) Graph simplification started 0:02:23.980 152M / 11G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:02:23.981 152M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:02:23.981 152M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:24.021 152M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 542 times 0:02:24.026 152M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:28.763 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 38243 times 0:02:28.776 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:28.862 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 249 times 0:02:28.863 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:02:28.863 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:28.887 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:02:28.888 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:28.914 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19 times 0:02:28.914 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:29.036 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1782 times 0:02:29.036 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:02:29.037 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:29.039 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times 0:02:29.039 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:29.176 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 449 times 0:02:29.176 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:29.199 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 345 times 0:02:29.200 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:02:29.200 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:29.202 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:02:29.207 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:29.232 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 97 times 0:02:29.232 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:29.238 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 145 times 0:02:29.239 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:02:29.239 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:29.239 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:29.240 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:29.266 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 58 times 0:02:29.280 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:29.291 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 78 times 0:02:29.297 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:02:29.297 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:29.297 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:29.297 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:29.303 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 29 times 0:02:29.304 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:29.309 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 99 times 0:02:29.309 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:02:29.309 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:29.310 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:29.310 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:29.317 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 37 times 0:02:29.317 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:29.332 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 191 times 0:02:29.332 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:02:29.333 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:29.333 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:02:29.333 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:29.346 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 53 times 0:02:29.346 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:29.368 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 400 times 0:02:29.368 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:02:29.368 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:29.369 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:29.369 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:29.395 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 127 times 0:02:29.395 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:29.446 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 719 times 0:02:29.446 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:02:29.446 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:29.447 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:29.448 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:29.530 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 218 times 0:02:29.530 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:29.595 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1025 times 0:02:29.595 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:02:29.596 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:29.648 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:29.648 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:30.122 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 332 times 0:02:30.122 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:30.158 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:02:30.158 156M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:02:30.158 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:30.159 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:30.159 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:30.159 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:30.160 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:30.160 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:02:30.160 156M / 11G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:02:30.160 156M / 11G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:02:30.160 156M / 11G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:02:30.160 156M / 11G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:02:30.160 156M / 11G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:02:30.161 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:30.193 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:30.194 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:30.604 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times 0:02:30.604 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:30.629 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:30.630 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:31.089 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:31.089 156M / 11G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:02:31.204 156M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:02:31.227 156M / 11G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 357 times 0:02:31.227 156M / 11G INFO General (simplification.cpp : 470) Counting average coverage 0:02:31.290 156M / 11G INFO General (simplification.cpp : 476) Average coverage = 68.7718 0:02:31.291 156M / 11G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:02:31.291 156M / 11G INFO General (contig_output_stage.cpp : 40) Writing GFA to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K33/assembly_graph_with_scaffolds.gfa 0:02:32.017 156M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K33/before_rr.fasta 0:02:32.975 156M / 11G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K33/assembly_graph.fastg 0:02:36.021 156M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K33/simplified_contigs.fasta 0:02:36.961 156M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K33/final_contigs.fasta 0:02:38.011 156M / 11G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:02:38.011 156M / 11G INFO General (contig_output_stage.cpp : 40) Writing GFA to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K33/assembly_graph_with_scaffolds.gfa 0:02:38.793 156M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K33/before_rr.fasta 0:02:39.812 156M / 11G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K33/assembly_graph.fastg 0:02:43.107 156M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K33/simplified_contigs.fasta 0:02:44.171 156M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K33/final_contigs.fasta 0:02:45.363 156M / 11G INFO General (launch.hpp : 149) SPAdes finished 0:02:45.632 80M / 11G INFO General (main.cpp : 109) Assembling time: 0 hours 2 minutes 45 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /home/deren/Documents/genomics-course/session-11/notebooks/test-1/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 64 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/home/deren/Documents/genomics-course/session-11/notebooks/test-1/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 20 0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.001 4M / 4M INFO General (construction.cpp : 111) Max read length 100 0:00:00.001 4M / 4M INFO General (construction.cpp : 117) Average read length 96.4783 0:00:00.001 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 400 files using 20 threads. This might take a while. 0:00:00.001 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.0666 Gb 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 83886 0:00:23.696 11G / 11G INFO General (kmer_splitters.hpp : 289) Processed 31348229 reads 0:00:34.912 11G / 11G INFO General (kmer_splitters.hpp : 289) Processed 43929778 reads 0:00:34.912 11G / 11G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:43.451 80M / 11G INFO General (kmer_splitters.hpp : 308) Used 43929778 reads 0:00:43.451 80M / 11G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:46.453 80M / 11G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 26939300 kmers in total. 0:00:46.453 80M / 11G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:46.997 80M / 11G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:46.997 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:46.997 80M / 11G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 320 files using 20 threads. This might take a while. 0:00:46.997 80M / 11G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:46.997 80M / 11G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.06536 Gb 0:00:46.997 80M / 11G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:00:51.504 11G / 11G INFO General (kmer_splitters.hpp : 380) Processed 26939300 kmers 0:00:51.504 11G / 11G INFO General (kmer_splitters.hpp : 385) Used 26939300 kmers. 0:00:51.716 80M / 11G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:53.271 80M / 11G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 26903805 kmers in total. 0:00:53.271 80M / 11G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:53.801 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:55.343 80M / 11G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:58.333 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 12483304 bytes occupied (3.71198 bits per kmer). 0:00:58.379 108M / 11G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:01:00.861 108M / 11G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:01:00.861 108M / 11G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:01:01.037 108M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:01:04.554 132M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 687107 sequences extracted 0:01:06.299 132M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:01:07.049 136M / 11G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 1 loops collected 0:01:07.817 304M / 11G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:01:07.818 304M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:07.818 304M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:09.166 336M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 12501992 bytes occupied (3.71264 bits per kmer). 0:01:09.284 440M / 11G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:01:42.864 436M / 11G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:01:45.230 436M / 11G INFO General (construction.cpp : 464) Processed 1373480 edges 0:01:45.433 272M / 11G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:01:45.434 272M / 11G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 2 0:01:45.434 272M / 11G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 29 0:01:45.434 272M / 11G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 30. Coverage mad: 11.8608 0:01:45.434 272M / 11G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:01:45.510 272M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:01:45.692 272M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:01:46.438 272M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:01:47.740 272M / 11G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:01:48.749 260M / 11G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 30.4802. Fitted coverage std. dev: 10.4434 0:01:48.751 260M / 11G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.802554 0:01:48.752 260M / 11G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 12 0:01:48.752 260M / 11G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 12 0:01:48.752 260M / 11G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 22268383 0:01:48.752 260M / 11G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 30.4802 0:01:48.753 260M / 11G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 12 0:01:48.753 260M / 11G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:01:48.753 260M / 11G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:01:48.753 260M / 11G INFO General (graph_pack.hpp : 101) Index refill 0:01:48.754 260M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:01:48.754 260M / 11G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 320 files using 20 threads. This might take a while. 0:01:48.754 260M / 11G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:01:48.755 260M / 11G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.06243 Gb 0:01:48.755 260M / 11G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:01:51.724 11G / 11G INFO General (edge_index_builders.hpp : 77) Processed 1373480 edges 0:01:51.724 11G / 11G INFO General (edge_index_builders.hpp : 82) Used 1373480 sequences. 0:01:51.860 256M / 11G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:01:53.583 256M / 11G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 26939300 kmers in total. 0:01:53.583 256M / 11G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:01:56.315 256M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:57.837 276M / 11G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:02:00.674 276M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 12499672 bytes occupied (3.71195 bits per kmer). 0:02:01.162 896M / 11G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:02:02.758 896M / 11G INFO General (edge_index.hpp : 92) Index refilled 0:02:02.758 896M / 11G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:02:03.592 940M / 11G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:02:15.014 948M / 11G INFO General (gap_closer.cpp : 138) Used 10942735 paired reads 0:02:15.014 948M / 11G INFO General (gap_closer.cpp : 140) Merging paired indices 0:02:15.158 904M / 11G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:02:17.184 904M / 11G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 6 gaps after checking 254 candidates 0:02:17.287 904M / 11G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:02:17.352 268M / 11G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:02:17.352 268M / 11G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled 0:02:17.352 268M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:02:17.471 268M / 11G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:02:17.471 268M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:02:23.492 284M / 11G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 237479 times 0:02:23.493 284M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:02:23.951 284M / 11G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 7569 times 0:02:23.952 284M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:02:24.184 284M / 11G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 29151 times 0:02:24.201 284M / 11G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:02:24.202 284M / 11G INFO General (simplification.cpp : 357) Graph simplification started 0:02:24.202 284M / 11G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:02:24.202 284M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:02:24.202 284M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:24.293 284M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 837 times 0:02:24.293 284M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:39.436 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 30988 times 0:02:39.436 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:39.471 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:02:39.471 456M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:02:39.471 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:39.493 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:02:39.494 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:39.494 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:39.494 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:39.515 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 187 times 0:02:39.516 456M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:02:39.516 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:39.517 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 16 times 0:02:39.517 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:39.547 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 51 times 0:02:39.547 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:39.582 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 400 times 0:02:39.582 456M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:02:39.583 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:39.584 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 22 times 0:02:39.584 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:39.645 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 99 times 0:02:39.646 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:39.651 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 114 times 0:02:39.652 456M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:02:39.652 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:39.653 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times 0:02:39.653 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:39.674 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 37 times 0:02:39.675 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:39.679 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 80 times 0:02:39.679 456M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:02:39.679 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:39.680 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times 0:02:39.680 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:39.693 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 22 times 0:02:39.694 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:39.699 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 89 times 0:02:39.700 456M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:02:39.700 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:39.700 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:39.700 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:39.713 456M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19 times 0:02:39.713 456M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:39.721 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 123 times 0:02:39.721 460M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:02:39.721 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:39.722 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:02:39.722 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:39.739 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 32 times 0:02:39.739 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:39.754 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 251 times 0:02:39.754 460M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:02:39.754 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:39.755 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:39.755 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:39.797 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 59 times 0:02:39.797 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:39.839 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 456 times 0:02:39.839 460M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:02:39.840 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:39.841 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:39.841 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:39.925 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 117 times 0:02:39.926 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:40.000 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 704 times 0:02:40.000 460M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:02:40.001 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:40.015 460M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:40.015 460M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:40.541 452M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 225 times 0:02:40.541 452M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:40.579 452M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:02:40.579 452M / 11G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12 0:02:40.579 452M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:02:40.580 452M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:02:40.580 452M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:02:40.580 452M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:02:40.580 452M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:02:40.580 452M / 11G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:02:40.580 452M / 11G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:02:40.580 452M / 11G INFO General (graph_pack.hpp : 101) Index refill 0:02:40.580 452M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:02:40.580 452M / 11G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 320 files using 20 threads. This might take a while. 0:02:40.581 452M / 11G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:02:40.581 452M / 11G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.05931 Gb 0:02:40.581 452M / 11G INFO General (kmer_splitters.hpp : 97) Using cell size of 104857 0:02:42.801 11G / 11G INFO General (edge_index_builders.hpp : 77) Processed 135416 edges 0:02:42.801 11G / 11G INFO General (edge_index_builders.hpp : 82) Used 135416 sequences. 0:02:42.934 448M / 11G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:02:44.250 448M / 11G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 20971423 kmers in total. 0:02:44.250 448M / 11G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:02:45.990 448M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:02:47.194 464M / 11G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:02:49.586 464M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9732688 bytes occupied (3.71274 bits per kmer). 0:02:50.168 944M / 11G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:02:51.535 944M / 11G INFO General (edge_index.hpp : 92) Index refilled 0:02:51.535 944M / 11G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:02:51.604 944M / 11G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:03:09.316 936M / 11G INFO General (gap_closer.cpp : 138) Used 10942735 paired reads 0:03:09.316 936M / 11G INFO General (gap_closer.cpp : 140) Merging paired indices 0:03:09.316 936M / 11G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:03:09.490 936M / 11G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1 gaps after checking 14 candidates 0:03:09.518 936M / 11G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:03:09.518 936M / 11G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:03:09.518 936M / 11G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled 0:03:09.518 936M / 11G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled 0:03:09.518 936M / 11G INFO General (graph_simplification.hpp : 634) Creating parallel br instance 0:03:09.518 936M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:03:09.547 936M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:03:09.547 936M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:03:09.956 936M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times 0:03:09.956 936M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:03:09.979 936M / 11G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:03:09.980 936M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:03:10.361 940M / 11G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:03:10.361 940M / 11G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:03:10.467 940M / 11G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:03:10.540 940M / 11G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 48 times 0:03:10.540 940M / 11G INFO General (simplification.cpp : 470) Counting average coverage 0:03:10.584 940M / 11G INFO General (simplification.cpp : 476) Average coverage = 43.3641 0:03:10.585 940M / 11G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:03:10.585 940M / 11G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 4194548 kmers to process 0:03:14.353 940M / 11G INFO General (graph_pack.hpp : 111) Normalizing done 0:04:16.953 1G / 11G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:04:19.323 968M / 11G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:04:19.460 940M / 11G INFO General (mismatch_correction.cpp : 27) Corrected 64 nucleotides 0:04:19.461 940M / 11G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:04:19.462 940M / 11G INFO General (contig_output_stage.cpp : 40) Writing GFA to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K55/assembly_graph_with_scaffolds.gfa 0:04:20.194 936M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K55/before_rr.fasta 0:04:21.073 936M / 11G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K55/assembly_graph.fastg 0:04:24.402 936M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K55/simplified_contigs.fasta 0:04:25.407 936M / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K55/intermediate_contigs.fasta 0:04:26.231 936M / 11G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:04:26.710 952M / 11G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 4198924 kmers to process 0:04:30.729 952M / 11G INFO General (graph_pack.hpp : 111) Normalizing done 0:04:30.814 952M / 11G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 23653 0:04:30.828 952M / 11G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0 0:04:30.829 952M / 11G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:04:31.124 1G / 11G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:04:38.223 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:04:38.428 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:04:38.541 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:04:38.606 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:04:38.707 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:04:38.806 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:04:39.384 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:04:45.444 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:04:54.592 1G / 11G INFO General (sequence_mapper_notifier.h: 98) Total 10942735 reads processed 0:04:56.304 1G / 11G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:04:56.304 1G / 11G INFO General (pair_info_count.cpp : 213) 4718332 paired reads (43.1184% of all) aligned to long edges 0:04:56.338 952M / 11G INFO General (pair_info_count.cpp : 354) Insert size = 349.156, deviation = 64.2412, left quantile = 274, right quantile = 417, read length = 100 0:04:56.473 1G / 11G INFO General (pair_info_count.cpp : 371) Filtering data for library #0 0:04:56.474 1G / 11G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:05:04.281 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:05:04.290 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:05:04.314 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:05:04.355 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:05:04.369 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:05:04.372 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:05:04.511 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:05:11.953 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:05:19.462 1G / 11G INFO General (sequence_mapper_notifier.h: 98) Total 10942735 reads processed 0:05:19.463 1G / 11G INFO General (pair_info_count.cpp : 383) Mapping library #0 0:05:19.463 1G / 11G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while) 0:05:19.463 1G / 11G INFO General (pair_info_count.cpp : 289) Left insert size quantile 274, right insert size quantile 417, filtering threshold 2, rounding threshold 0 0:05:19.477 1G / 11G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:05:29.781 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads 0:05:30.207 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads 0:05:30.331 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads 0:05:30.450 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads 0:05:30.563 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads 0:05:30.622 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads 0:05:30.898 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads 0:05:40.831 1G / 11G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads 0:05:50.753 1G / 11G INFO General (sequence_mapper_notifier.h: 98) Total 10942735 reads processed 0:05:50.820 1G / 11G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:05:50.820 1G / 11G INFO General (distance_estimation.cpp : 173) Processing library #0 0:05:50.820 1G / 11G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:05:50.820 1G / 11G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:08:36.895 1G / 11G INFO General (distance_estimation.cpp : 34) Filtering info 0:08:36.895 1G / 11G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 14875296 0:08:46.700 1G / 11G INFO General (pair_info_filters.hpp : 263) Done filtering 0:08:46.712 1G / 11G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:08:49.400 1G / 11G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:08:49.400 1G / 11G INFO General (distance_estimation.cpp : 160) Improving paired information 0:09:16.981 1G / 11G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1601740; contradictional = 7160 0:09:44.872 2G / 11G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 258942; contradictional = 262 0:09:44.872 2G / 11G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 0:09:44.872 2G / 11G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:12:23.500 2G / 11G INFO General (distance_estimation.cpp : 34) Filtering info 0:12:23.500 2G / 11G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 555043 0:12:23.882 2G / 11G INFO General (pair_info_filters.hpp : 263) Done filtering 0:12:23.884 2G / 11G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 0:12:25.900 1G / 11G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:12:25.900 1G / 11G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:12:25.900 1G / 11G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started 0:12:26.440 2G / 11G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:12:26.441 2G / 11G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 43.3641 0:12:26.456 2G / 11G INFO General (extenders_logic.cpp : 275) Estimated coverage of library #0 is 43.3641 0:12:26.538 2G / 11G INFO General (extenders_logic.cpp : 472) Using 1 paired-end library 0:12:26.538 2G / 11G INFO General (extenders_logic.cpp : 473) Using 1 paired-end scaffolding library 0:12:26.539 2G / 11G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries 0:12:26.539 2G / 11G INFO General (launcher.cpp : 420) Total number of extenders is 3 0:12:26.539 2G / 11G INFO General (path_extender.hpp : 885) Processed 0 paths from 67341 (0%) 0:12:26.998 2G / 11G INFO General (path_extender.hpp : 883) Processed 128 paths from 67341 (0%) 0:12:27.317 2G / 11G INFO General (path_extender.hpp : 883) Processed 256 paths from 67341 (0%) 0:12:27.930 2G / 11G INFO General (path_extender.hpp : 883) Processed 512 paths from 67341 (0%) 0:12:28.516 2G / 11G INFO General (path_extender.hpp : 883) Processed 1024 paths from 67341 (1%) 0:12:32.368 2G / 11G INFO General (path_extender.hpp : 883) Processed 2048 paths from 67341 (3%) 0:12:41.000 2G / 11G INFO General (path_extender.hpp : 883) Processed 4096 paths from 67341 (6%) 0:12:47.815 2G / 11G INFO General (path_extender.hpp : 885) Processed 6735 paths from 67341 (10%) 0:12:48.812 2G / 11G INFO General (path_extender.hpp : 883) Processed 8192 paths from 67341 (12%) 0:12:51.170 2G / 11G INFO General (path_extender.hpp : 885) Processed 13470 paths from 67341 (20%) 0:12:52.007 2G / 11G INFO General (path_extender.hpp : 883) Processed 16384 paths from 67341 (24%) 0:12:52.847 2G / 11G INFO General (path_extender.hpp : 885) Processed 20205 paths from 67341 (30%) 0:12:53.827 2G / 11G INFO General (path_extender.hpp : 885) Processed 26940 paths from 67341 (40%) 0:12:54.460 2G / 11G INFO General (path_extender.hpp : 883) Processed 32768 paths from 67341 (48%) 0:12:54.582 2G / 11G INFO General (path_extender.hpp : 885) Processed 33675 paths from 67341 (50%) 0:12:55.351 2G / 11G INFO General (path_extender.hpp : 885) Processed 40410 paths from 67341 (60%) 0:12:55.906 2G / 11G INFO General (path_extender.hpp : 885) Processed 47145 paths from 67341 (70%) 0:12:56.375 2G / 11G INFO General (path_extender.hpp : 885) Processed 53880 paths from 67341 (80%) 0:12:56.816 2G / 11G INFO General (path_extender.hpp : 885) Processed 60615 paths from 67341 (90%) 0:12:57.125 2G / 11G INFO General (path_extender.hpp : 883) Processed 65536 paths from 67341 (97%) 0:12:57.203 2G / 11G INFO General (launcher.cpp : 234) Finalizing paths 0:12:57.204 2G / 11G INFO General (launcher.cpp : 236) Deduplicating paths 0:12:57.945 2G / 11G INFO General (launcher.cpp : 240) Paths deduplicated 0:12:57.946 2G / 11G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:12:57.946 2G / 11G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:12:58.045 2G / 11G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:12:58.046 2G / 11G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:12:58.704 2G / 11G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:12:59.405 2G / 11G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:12:59.526 2G / 11G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:12:59.618 2G / 11G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:12:59.909 2G / 11G INFO General (launcher.cpp : 257) Paths finalized 0:12:59.910 2G / 11G INFO General (launcher.cpp : 427) Closing gaps in paths 0:13:00.387 2G / 11G INFO General (launcher.cpp : 455) Gap closing completed 0:13:00.545 2G / 11G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:13:01.502 2G / 11G INFO General (launcher.cpp : 296) Traversed 150 loops 0:13:01.503 2G / 11G INFO General (launcher.cpp : 234) Finalizing paths 0:13:01.503 2G / 11G INFO General (launcher.cpp : 236) Deduplicating paths 0:13:01.578 2G / 11G INFO General (launcher.cpp : 240) Paths deduplicated 0:13:01.578 2G / 11G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:13:01.578 2G / 11G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:13:01.674 2G / 11G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:13:01.674 2G / 11G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:13:01.814 2G / 11G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:13:01.961 2G / 11G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:13:01.976 2G / 11G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:13:02.059 2G / 11G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:13:02.275 2G / 11G INFO General (launcher.cpp : 257) Paths finalized 0:13:02.636 2G / 11G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished 0:13:03.617 2G / 11G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:13:03.617 2G / 11G INFO General (contig_output_stage.cpp : 40) Writing GFA to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K55/assembly_graph_with_scaffolds.gfa 0:13:04.300 2G / 11G INFO General (contig_output.hpp : 22) Outputting contigs to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K55/before_rr.fasta 0:13:05.185 2G / 11G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K55/assembly_graph.fastg 0:13:08.749 2G / 11G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K55/final_contigs.paths 0:13:10.059 2G / 11G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /home/deren/Documents/genomics-course/session-11/notebooks/test-1//K55/scaffolds.paths 0:13:11.413 2G / 11G INFO General (launch.hpp : 149) SPAdes finished 0:13:15.608 84M / 11G INFO General (main.cpp : 109) Assembling time: 0 hours 13 minutes 15 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 * Corrected reads are in /home/deren/Documents/genomics-course/session-11/notebooks/test-1/corrected/ * Assembled contigs are in /home/deren/Documents/genomics-course/session-11/notebooks/test-1/contigs.fasta * Assembled scaffolds are in /home/deren/Documents/genomics-course/session-11/notebooks/test-1/scaffolds.fasta * Assembly graph is in /home/deren/Documents/genomics-course/session-11/notebooks/test-1/assembly_graph.fastg * Assembly graph in GFA format is in /home/deren/Documents/genomics-course/session-11/notebooks/test-1/assembly_graph_with_scaffolds.gfa * Paths in the assembly graph corresponding to the contigs are in /home/deren/Documents/genomics-course/session-11/notebooks/test-1/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /home/deren/Documents/genomics-course/session-11/notebooks/test-1/scaffolds.paths ======= SPAdes pipeline finished. SPAdes log can be found here: /home/deren/Documents/genomics-course/session-11/notebooks/test-1/spades.log Thank you for using SPAdes!