Created
February 11, 2019 14:11
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SPAdes issued log
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| Command line: /cm/shared/c3ddb/SPAdes/3.6.2/bin/spades.py --careful --sc -t 8 -m 64 -1 /scratch/users/yehang/mock/28625_R1_paired.fastq -2 /scratch/users/yehang/mock/28625_R2_paired.fastq -o /scratch/users/yehang/individual/results/28625 | |
| System information: | |
| SPAdes version: 3.6.2 | |
| Python version: 2.6.6 | |
| OS: Linux-2.6.32-431.el6.x86_64-x86_64-with-redhat-6.6-Santiago | |
| Output dir: /scratch/users/yehang/individual/results/28625 | |
| Mode: read error correction and assembling | |
| Debug mode is turned OFF | |
| Dataset parameters: | |
| Single-cell mode | |
| Reads: | |
| Library number: 1, library type: paired-end | |
| orientation: fr | |
| left reads: ['/scratch/users/yehang/mock/28625_R1_paired.fastq'] | |
| right reads: ['/scratch/users/yehang/mock/28625_R2_paired.fastq'] | |
| interlaced reads: not specified | |
| single reads: not specified | |
| Read error correction parameters: | |
| Iterations: 1 | |
| PHRED offset will be auto-detected | |
| Corrected reads will be compressed (with gzip) | |
| Assembly parameters: | |
| k: [21, 33, 55] | |
| Mismatch careful mode is turned ON | |
| Repeat resolution is enabled | |
| MismatchCorrector will be used | |
| Coverage cutoff is turned OFF | |
| Other parameters: | |
| Dir for temp files: /scratch/users/yehang/individual/results/28625/tmp | |
| Threads: 8 | |
| Memory limit (in Gb): 64 | |
| ======= SPAdes pipeline started. Log can be found here: /scratch/users/yehang/individual/results/28625/spades.log | |
| ===== Read error correction started. | |
| == Running read error correction tool: /cm/shared/c3ddb/SPAdes/3.6.2/bin/hammer /scratch/users/yehang/individual/results/28625/corrected/configs/config.info | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 83) Starting BayesHammer, built from refs/heads/spades_3.6.2, git revision ed2c9d8f9dffb948d560432820a834bb60c8de8d | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Loading config from /scratch/users/yehang/individual/results/28625/corrected/configs/config.info | |
| 0:00:00.002 4M / 4M INFO General (memory_limit.hpp : 43) Memory limit set to 64 Gb | |
| 0:00:00.002 4M / 4M INFO General (main.cpp : 93) Trying to determine PHRED offset | |
| 0:00:00.007 4M / 4M INFO General (main.cpp : 99) Determined value is 33 | |
| 0:00:00.008 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] | |
| 0:00:00.008 4M / 4M INFO General (main.cpp : 120) Size of aux. kmer data 24 bytes | |
| === ITERATION 0 begins === | |
| 0:00:00.008 4M / 4M INFO K-mer Index Building (kmer_index.hpp : 464) Building kmer index | |
| 0:00:00.008 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 141) Splitting kmer instances into 128 buckets. This might take a while. | |
| 0:00:00.008 4M / 4M INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:00.008 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 159) Memory available for splitting buffers: 2.6665 Gb | |
| 0:00:00.008 4M / 4M INFO K-mer Splitting (kmer_data.cpp : 167) Using cell size of 524288 | |
| 0:00:00.009 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processing /scratch/users/yehang/mock/28625_R1_paired.fastq | |
| 0:00:00.540 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 181) Processing /scratch/users/yehang/mock/28625_R2_paired.fastq | |
| 0:00:00.908 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 190) Processed 48852 reads | |
| 0:00:00.908 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 195) Processed 48852 reads | |
| 0:00:00.921 32M / 8G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:01.069 32M / 8G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 304338 kmers in total. | |
| 0:00:01.069 32M / 8G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:01.280 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 473) Building perfect hash indices | |
| 0:00:01.303 32M / 8G INFO General (kmer_index.hpp : 368) Merging final buckets. | |
| 0:00:01.347 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 521) Index built. Total 99544 bytes occupied (2.61667 bits per kmer). | |
| 0:00:01.348 32M / 8G INFO K-mer Counting (kmer_data.cpp : 280) Arranging kmers in hash map order | |
| 0:00:01.476 36M / 8G INFO General (main.cpp : 155) Clustering Hamming graph. | |
| 0:00:01.477 36M / 8G INFO Hamming Clustering (hamcluster.cpp : 120) Serializing sub-kmers. | |
| 0:00:01.477 36M / 8G INFO Hamming Clustering (hamcluster.cpp : 125) Serializing: [0, 10) | |
| 0:00:01.592 36M / 8G INFO Hamming Clustering (hamcluster.cpp : 125) Serializing: [10, 21) | |
| 0:00:01.707 36M / 8G INFO Hamming Clustering (hamcluster.cpp : 137) Splitting sub-kmers, pass 1. | |
| 0:00:02.386 36M / 8G INFO Hamming Clustering (hamcluster.cpp : 162) Splitting done. Processed 2 blocks. Produced 266786 blocks. | |
| 0:00:02.387 36M / 8G INFO Hamming Clustering (hamcluster.cpp : 171) Merge done, total 1688 new blocks generated. | |
| 0:00:02.387 36M / 8G INFO Hamming Clustering (hamcluster.cpp : 176) Spliting sub-kmers, pass 2. | |
| 0:00:02.848 36M / 8G INFO Hamming Clustering (hamcluster.cpp : 195) Splitting done. Processed 3376 blocks. Produced 104346 blocks. | |
| 0:00:02.848 36M / 8G INFO Hamming Clustering (hamcluster.cpp : 202) Merge done, saw 1 big blocks out of 104346 processed. | |
| 0:00:02.948 36M / 8G INFO General (main.cpp : 169) Clustering done. Total clusters: 115552 | |
| 0:00:02.949 32M / 8G INFO K-mer Counting (kmer_data.cpp : 295) Collecting K-mer information, this takes a while. | |
| 0:00:02.954 40M / 8G INFO K-mer Counting (kmer_data.cpp : 301) Processing /scratch/users/yehang/mock/28625_R1_paired.fastq | |
| 0:00:03.300 40M / 8G INFO K-mer Counting (kmer_data.cpp : 301) Processing /scratch/users/yehang/mock/28625_R2_paired.fastq | |
| 0:00:04.110 40M / 8G INFO K-mer Counting (kmer_data.cpp : 308) Collection done, postprocessing. | |
| 0:00:04.114 40M / 8G INFO K-mer Counting (kmer_data.cpp : 321) There are 304338 kmers in total. Among them 238844 (78.4798%) are singletons. | |
| 0:00:04.114 40M / 8G INFO General (main.cpp : 175) Subclustering Hamming graph | |
| 0:00:04.382 40M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 647) Subclustering done. Total 0 non-read kmers were generated. | |
| 0:00:04.382 40M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 648) Subclustering statistics: | |
| 0:00:04.382 40M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Total singleton hamming clusters: 113058. Among them 1406 (1.24361%) are good | |
| 0:00:04.382 40M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Total singleton subclusters: 16. Among them 16 (100%) are good | |
| 0:00:04.382 40M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total non-singleton subcluster centers: 6445. Among them 5107 (79.2397%) are good | |
| 0:00:04.382 40M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Average size of non-trivial subcluster: 29.6788 kmers | |
| 0:00:04.382 40M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Average number of sub-clusters per non-singleton cluster: 2.59062 | |
| 0:00:04.382 40M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Total solid k-mers: 6529 | |
| 0:00:04.382 40M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Substitution probabilities: [4,4]((0.91951,0.0288172,0.0252331,0.0264399),(0.0271257,0.927317,0.0316877,0.0138699),(0.0136321,0.0314172,0.927592,0.0273592),(0.0264029,0.0250619,0.02873,0.919805)) | |
| 0:00:04.384 40M / 8G INFO General (main.cpp : 180) Finished clustering. | |
| 0:00:04.384 40M / 8G INFO General (main.cpp : 199) Starting solid k-mers expansion in 8 threads. | |
| 0:00:04.695 40M / 8G INFO General (main.cpp : 220) Solid k-mers iteration 0 produced 5521 new k-mers. | |
| 0:00:05.002 40M / 8G INFO General (main.cpp : 220) Solid k-mers iteration 1 produced 958 new k-mers. | |
| 0:00:05.310 40M / 8G INFO General (main.cpp : 220) Solid k-mers iteration 2 produced 6 new k-mers. | |
| 0:00:05.311 40M / 8G INFO General (main.cpp : 224) Solid k-mers finalized | |
| 0:00:05.311 40M / 8G INFO General (hammer_tools.cpp : 210) Starting read correction in 8 threads. | |
| 0:00:05.311 40M / 8G INFO General (hammer_tools.cpp : 221) Correcting pair of reads: /scratch/users/yehang/mock/28625_R1_paired.fastq and /scratch/users/yehang/mock/28625_R2_paired.fastq | |
| 0:00:05.510 124M / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 24426 reads. | |
| 0:00:06.667 124M / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0 | |
| 0:00:06.880 124M / 8G INFO General (hammer_tools.cpp : 185) Written batch 0 | |
| 0:00:06.927 40M / 8G INFO General (hammer_tools.cpp : 269) Correction done. Changed 13469 bases in 7164 reads. | |
| 0:00:06.927 40M / 8G INFO General (hammer_tools.cpp : 270) Failed to correct 2715 bases out of 5338581. | |
| 0:00:06.928 32M / 8G INFO General (main.cpp : 257) Saving corrected dataset description to /scratch/users/yehang/individual/results/28625/corrected/corrected.yaml | |
| 0:00:06.929 32M / 8G INFO General (main.cpp : 264) All done. Exiting. | |
| == Compressing corrected reads (with gzip) | |
| == Dataset description file was created: /scratch/users/yehang/individual/results/28625/corrected/corrected.yaml | |
| ===== Read error correction finished. | |
| ===== Assembling started. | |
| == Running assembler: K21 | |
| 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 43) Memory limit set to 64 Gb | |
| 0:00:00.001 4M / 4M INFO General (main.cpp : 147) Starting SPAdes, built from refs/heads/spades_3.6.2, git revision ed2c9d8f9dffb948d560432820a834bb60c8de8d | |
| 0:00:00.001 4M / 4M INFO General (main.cpp : 148) Assembling dataset (/scratch/users/yehang/individual/results/28625/dataset.info) with K=21 | |
| 0:00:00.002 4M / 4M INFO General (launch.hpp : 30) SPAdes started | |
| 0:00:00.002 4M / 4M INFO General (launch.hpp : 31) Starting from stage: construction | |
| 0:00:00.002 4M / 4M INFO General (launch.hpp : 39) Two-step RR enabled: 0 | |
| 0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction | |
| 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 79) Converting reads to binary format (takes a while) | |
| 0:00:00.005 4M / 4M INFO General (read_converter.hpp : 81) Paired reads for library #0 | |
| 0:00:00.970 80M / 80M INFO General (binary_converter.hpp : 139) 16384 reads processed | |
| 0:00:01.176 84M / 84M INFO General (binary_converter.hpp : 159) 23458 reads written | |
| 0:00:01.207 4M / 84M INFO General (read_converter.hpp : 91) Single reads for library #0 | |
| 0:00:02.702 132M / 148M INFO General (binary_converter.hpp : 159) 915 reads written | |
| 0:00:02.712 4M / 148M INFO General (graph_construction.hpp : 130) Constructing DeBruijn graph for k=21 | |
| 0:00:02.714 4M / 148M INFO General (kmer_splitters.hpp : 179) Splitting kmer instances into 64 buckets. This might take a while. | |
| 0:00:02.714 4M / 148M INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:02.714 4M / 148M INFO General (kmer_splitters.hpp : 197) Memory available for splitting buffers: 2.6665 Gb | |
| 0:00:02.715 4M / 148M INFO General (kmer_splitters.hpp : 206) Using cell size of 1048576 | |
| 0:00:03.197 6G / 6G INFO General (kmer_splitters.hpp : 235) Processed 95662 reads | |
| 0:00:03.197 6G / 6G INFO General (kmer_splitters.hpp : 241) Adding contigs from previous K | |
| 0:00:03.198 6G / 6G INFO General (kmer_splitters.hpp : 252) Used 95662 reads. Maximum read length 150 | |
| 0:00:03.198 6G / 6G INFO General (kmer_splitters.hpp : 253) Average read length 110.578 | |
| 0:00:03.205 32M / 6G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:03.317 32M / 6G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 63350 kmers in total. | |
| 0:00:03.317 32M / 6G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:03.415 32M / 6G INFO K-mer Index Building (kmer_index.hpp : 464) Building kmer index | |
| 0:00:03.416 32M / 6G INFO General (kmer_splitters.hpp : 386) Splitting kmer instances into 128 buckets. This might take a while. | |
| 0:00:03.416 32M / 6G INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:03.416 32M / 6G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 2.66536 Gb | |
| 0:00:03.416 32M / 6G INFO General (kmer_splitters.hpp : 412) Using cell size of 524288 | |
| 0:00:03.880 8G / 8G INFO General (kmer_splitters.hpp : 435) Processed 63350 kmers | |
| 0:00:03.880 8G / 8G INFO General (kmer_splitters.hpp : 444) Used 63350 kmers. | |
| 0:00:03.894 32M / 8G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:04.039 32M / 8G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 62077 kmers in total. | |
| 0:00:04.039 32M / 8G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:04.232 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 473) Building perfect hash indices | |
| 0:00:04.243 32M / 8G INFO General (kmer_index.hpp : 368) Merging final buckets. | |
| 0:00:04.273 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 521) Index built. Total 20432 bytes occupied (2.63312 bits per kmer). | |
| 0:00:04.273 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 391) Building k-mer extensions from k+1-mers | |
| 0:00:04.296 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 395) Building k-mer extensions from k+1-mers finished. | |
| 0:00:04.298 32M / 8G INFO Early tip clipping (early_simplification.hpp : 243) Early tip clipping | |
| 0:00:04.436 32M / 8G INFO Early tip clipping (early_simplification.hpp : 246) 23708 22-mers were removed by early tip clipper | |
| 0:00:04.436 32M / 8G INFO General (graph_construction.hpp : 146) Condensing graph | |
| 0:00:04.436 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 338) Extracting unbranching paths | |
| 0:00:04.515 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 352) Extracting unbranching paths finished. 7044 sequences extracted | |
| 0:00:04.523 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 312) Collecting perfect loops | |
| 0:00:04.552 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 327) Collecting perfect loops finished. 2 loops collected | |
| 0:00:04.566 32M / 8G INFO General (graph_construction.hpp : 151) Building index with from graph | |
| 0:00:04.566 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 464) Building kmer index | |
| 0:00:04.566 32M / 8G INFO General (kmer_splitters.hpp : 296) Splitting kmer instances into 16 buckets. This might take a while. | |
| 0:00:04.566 32M / 8G INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:04.566 32M / 8G INFO General (kmer_splitters.hpp : 314) Memory available for splitting buffers: 21.3229 Gb | |
| 0:00:04.566 32M / 8G INFO General (kmer_splitters.hpp : 319) Using cell size of 4194304 | |
| 0:00:04.634 608M / 8G INFO General (kmer_splitters.hpp : 332) Processed 7046 edges | |
| 0:00:04.634 608M / 8G INFO General (kmer_splitters.hpp : 337) Used 7046 sequences. | |
| 0:00:04.634 32M / 8G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:04.695 32M / 8G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 39642 kmers in total. | |
| 0:00:04.695 32M / 8G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:04.734 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 473) Building perfect hash indices | |
| 0:00:04.761 32M / 8G INFO General (kmer_index.hpp : 368) Merging final buckets. | |
| 0:00:04.788 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 521) Index built. Total 13072 bytes occupied (2.63801 bits per kmer). | |
| 0:00:04.789 32M / 8G INFO General (edge_index_builders.hpp : 28) Collecting k-mer coverage information from graph, this takes a while. | |
| 0:00:04.842 32M / 8G INFO General (graph_construction.hpp : 183) Filling coverage index | |
| 0:00:04.842 32M / 8G INFO General (edge_index_builders.hpp : 106) Collecting k-mer coverage information from reads, this takes a while. | |
| 0:00:05.314 32M / 8G INFO General (graph_construction.hpp : 185) Filling coverage and flanking coverage from index | |
| 0:00:05.316 32M / 8G INFO General (construction.cpp : 34) Figured out: read length = 150 | |
| 0:00:05.318 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding | |
| 0:00:05.322 32M / 8G INFO ThresholdFinder (omni_tools.hpp : 304) Bucket size: 37 | |
| 0:00:05.323 32M / 8G INFO ThresholdFinder (omni_tools.hpp : 319) Proper threshold was not found. Threshold set to 0.1 of average coverage | |
| 0:00:05.324 32M / 8G INFO General (genomic_info_filler.cpp : 76) Average edge coverage: 107.438 | |
| 0:00:05.324 32M / 8G INFO General (genomic_info_filler.cpp : 77) Graph threshold: 10.7438 | |
| 0:00:05.330 32M / 8G INFO General (genomic_info_filler.cpp : 119) EC coverage threshold value was calculated as 10.7438 | |
| 0:00:05.330 32M / 8G INFO General (genomic_info_filler.cpp : 120) Trusted kmer low bound: 0 | |
| 0:00:05.330 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == Simplification | |
| 0:00:05.331 32M / 8G INFO General (graph_simplification.hpp : 970) Graph simplification started | |
| 0:00:05.331 32M / 8G INFO General (graph_simplification.hpp : 975) Fast simplification mode disabled | |
| 0:00:05.331 32M / 8G INFO General (graph_simplification.hpp : 695) PROCEDURE == Presimplification | |
| 0:00:05.331 32M / 8G INFO General (graph_simplification.hpp : 213) Removing short low covered self-conjugate connections | |
| 0:00:05.332 32M / 8G INFO General (graph_simplification.hpp : 699) Further presimplification is disabled | |
| 0:00:05.332 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 1 | |
| 0:00:05.335 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.341 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.526 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:05.535 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 2 | |
| 0:00:05.536 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.539 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.611 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:05.614 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 3 | |
| 0:00:05.614 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.616 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.633 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:05.634 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 4 | |
| 0:00:05.634 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.636 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.643 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:05.644 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 5 | |
| 0:00:05.644 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.645 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.650 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:05.651 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 6 | |
| 0:00:05.651 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.652 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.656 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:05.656 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 7 | |
| 0:00:05.657 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.657 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.661 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:05.662 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 8 | |
| 0:00:05.662 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.663 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.667 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:05.667 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 9 | |
| 0:00:05.667 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.668 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.671 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:05.672 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 10 | |
| 0:00:05.672 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.673 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.675 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:05.676 32M / 8G INFO General (graph_simplification.hpp : 839) PROCEDURE == Post simplification | |
| 0:00:05.676 32M / 8G INFO General (graph_simplification.hpp : 856) Iteration 0 | |
| 0:00:05.676 32M / 8G INFO General (graph_simplification.hpp : 290) Clipping tips based on topology | |
| 0:00:05.676 32M / 8G INFO General (graph_simplification.hpp : 255) Removal of relatively low covered connections disabled | |
| 0:00:05.676 32M / 8G INFO General (graph_simplification.hpp : 530) Complex tip clipping disabled | |
| 0:00:05.677 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.677 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.678 32M / 8G INFO General (graph_simplification.hpp : 856) Iteration 1 | |
| 0:00:05.678 32M / 8G INFO General (graph_simplification.hpp : 290) Clipping tips based on topology | |
| 0:00:05.679 32M / 8G INFO General (graph_simplification.hpp : 255) Removal of relatively low covered connections disabled | |
| 0:00:05.679 32M / 8G INFO General (graph_simplification.hpp : 530) Complex tip clipping disabled | |
| 0:00:05.679 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:05.680 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:05.681 32M / 8G INFO General (graph_simplification.hpp : 392) Removing hidden erroneous connections | |
| 0:00:05.681 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup | |
| 0:00:05.682 32M / 8G INFO General (graph_simplification.hpp : 406) Removing isolated edges | |
| 0:00:05.682 32M / 8G INFO General (graph_simplification.hpp : 407) All edges shorter than 150 will be removed | |
| 0:00:05.682 32M / 8G INFO General (graph_simplification.hpp : 408) Also edges shorter than 0 and coverage smaller than 2 will be removed | |
| 0:00:05.684 32M / 8G INFO General (simplification.cpp : 88) Counting average coverage | |
| 0:00:05.684 32M / 8G INFO General (simplification.cpp : 91) Average coverage = 1545.45 | |
| 0:00:05.684 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == Contig Output | |
| 0:00:05.684 32M / 8G INFO General (contig_output.hpp : 297) Outputting contigs to /scratch/users/yehang/individual/results/28625//K21/simplified_contigs.fasta | |
| 0:00:05.700 32M / 8G INFO General (contig_output.hpp : 297) Outputting contigs to /scratch/users/yehang/individual/results/28625//K21/before_rr.fasta | |
| 0:00:05.715 32M / 8G INFO General (contig_output.hpp : 334) Outputting graph to /scratch/users/yehang/individual/results/28625//K21/assembly_graph.fastg | |
| 0:00:05.744 32M / 8G INFO General (contig_output.hpp : 297) Outputting contigs to /scratch/users/yehang/individual/results/28625//K21/final_contigs.fasta | |
| 0:00:05.763 32M / 8G INFO General (launch.hpp : 112) SPAdes finished | |
| 0:00:05.767 32M / 8G INFO General (main.cpp : 168) Assembling time: 0 hours 0 minutes 5 seconds | |
| == Running assembler: K33 | |
| 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 43) Memory limit set to 64 Gb | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 147) Starting SPAdes, built from refs/heads/spades_3.6.2, git revision ed2c9d8f9dffb948d560432820a834bb60c8de8d | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 148) Assembling dataset (/scratch/users/yehang/individual/results/28625/dataset.info) with K=33 | |
| 0:00:00.000 4M / 4M INFO General (launch.hpp : 30) SPAdes started | |
| 0:00:00.000 4M / 4M INFO General (launch.hpp : 31) Starting from stage: construction | |
| 0:00:00.000 4M / 4M INFO General (launch.hpp : 39) Two-step RR enabled: 0 | |
| 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction | |
| 0:00:00.001 4M / 4M INFO General (construction.cpp : 45) Contigs from previous K will be used | |
| 0:00:00.003 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected | |
| 0:00:00.006 4M / 4M INFO General (graph_construction.hpp : 130) Constructing DeBruijn graph for k=33 | |
| 0:00:00.008 4M / 4M INFO General (kmer_splitters.hpp : 179) Splitting kmer instances into 64 buckets. This might take a while. | |
| 0:00:00.008 4M / 4M INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:00.008 4M / 4M INFO General (kmer_splitters.hpp : 197) Memory available for splitting buffers: 2.6665 Gb | |
| 0:00:00.008 4M / 4M INFO General (kmer_splitters.hpp : 206) Using cell size of 524288 | |
| 0:00:00.424 6G / 6G INFO General (kmer_splitters.hpp : 235) Processed 95662 reads | |
| 0:00:00.424 6G / 6G INFO General (kmer_splitters.hpp : 241) Adding contigs from previous K | |
| 0:00:00.507 6G / 6G INFO General (kmer_splitters.hpp : 252) Used 95662 reads. Maximum read length 150 | |
| 0:00:00.507 6G / 6G INFO General (kmer_splitters.hpp : 253) Average read length 110.578 | |
| 0:00:00.514 32M / 6G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:00.589 32M / 6G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 74959 kmers in total. | |
| 0:00:00.589 32M / 6G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:00.693 32M / 6G INFO K-mer Index Building (kmer_index.hpp : 464) Building kmer index | |
| 0:00:00.693 32M / 6G INFO General (kmer_splitters.hpp : 386) Splitting kmer instances into 128 buckets. This might take a while. | |
| 0:00:00.693 32M / 6G INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:00.693 32M / 6G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 2.66536 Gb | |
| 0:00:00.693 32M / 6G INFO General (kmer_splitters.hpp : 412) Using cell size of 262144 | |
| 0:00:01.111 8G / 8G INFO General (kmer_splitters.hpp : 435) Processed 74959 kmers | |
| 0:00:01.111 8G / 8G INFO General (kmer_splitters.hpp : 444) Used 74959 kmers. | |
| 0:00:01.125 32M / 8G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:01.270 32M / 8G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 74171 kmers in total. | |
| 0:00:01.270 32M / 8G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:01.480 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 473) Building perfect hash indices | |
| 0:00:01.493 32M / 8G INFO General (kmer_index.hpp : 368) Merging final buckets. | |
| 0:00:01.528 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 521) Index built. Total 24400 bytes occupied (2.63176 bits per kmer). | |
| 0:00:01.528 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 391) Building k-mer extensions from k+1-mers | |
| 0:00:01.547 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 395) Building k-mer extensions from k+1-mers finished. | |
| 0:00:01.548 32M / 8G INFO Early tip clipping (early_simplification.hpp : 243) Early tip clipping | |
| 0:00:01.704 32M / 8G INFO Early tip clipping (early_simplification.hpp : 246) 33901 34-mers were removed by early tip clipper | |
| 0:00:01.704 32M / 8G INFO General (graph_construction.hpp : 146) Condensing graph | |
| 0:00:01.704 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 338) Extracting unbranching paths | |
| 0:00:01.788 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 352) Extracting unbranching paths finished. 6440 sequences extracted | |
| 0:00:01.795 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 312) Collecting perfect loops | |
| 0:00:01.832 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 327) Collecting perfect loops finished. 2 loops collected | |
| 0:00:01.837 32M / 8G INFO General (graph_construction.hpp : 151) Building index with from graph | |
| 0:00:01.838 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 464) Building kmer index | |
| 0:00:01.838 32M / 8G INFO General (kmer_splitters.hpp : 296) Splitting kmer instances into 16 buckets. This might take a while. | |
| 0:00:01.838 32M / 8G INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:01.838 32M / 8G INFO General (kmer_splitters.hpp : 314) Memory available for splitting buffers: 21.3229 Gb | |
| 0:00:01.838 32M / 8G INFO General (kmer_splitters.hpp : 319) Using cell size of 2097152 | |
| 0:00:01.889 608M / 8G INFO General (kmer_splitters.hpp : 332) Processed 6442 edges | |
| 0:00:01.889 608M / 8G INFO General (kmer_splitters.hpp : 337) Used 6442 sequences. | |
| 0:00:01.889 32M / 8G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:01.955 32M / 8G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 41058 kmers in total. | |
| 0:00:01.955 32M / 8G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:01.994 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 473) Building perfect hash indices | |
| 0:00:02.027 32M / 8G INFO General (kmer_index.hpp : 368) Merging final buckets. | |
| 0:00:02.055 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 521) Index built. Total 13576 bytes occupied (2.64523 bits per kmer). | |
| 0:00:02.057 32M / 8G INFO General (edge_index_builders.hpp : 28) Collecting k-mer coverage information from graph, this takes a while. | |
| 0:00:02.115 32M / 8G INFO General (graph_construction.hpp : 183) Filling coverage index | |
| 0:00:02.115 32M / 8G INFO General (edge_index_builders.hpp : 106) Collecting k-mer coverage information from reads, this takes a while. | |
| 0:00:02.549 32M / 8G INFO General (graph_construction.hpp : 185) Filling coverage and flanking coverage from index | |
| 0:00:02.551 32M / 8G INFO General (construction.cpp : 34) Figured out: read length = 150 | |
| 0:00:02.562 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding | |
| 0:00:02.565 32M / 8G INFO ThresholdFinder (omni_tools.hpp : 304) Bucket size: 31 | |
| 0:00:02.567 32M / 8G INFO ThresholdFinder (omni_tools.hpp : 319) Proper threshold was not found. Threshold set to 0.1 of average coverage | |
| 0:00:02.567 32M / 8G INFO General (genomic_info_filler.cpp : 76) Average edge coverage: 89.5378 | |
| 0:00:02.567 32M / 8G INFO General (genomic_info_filler.cpp : 77) Graph threshold: 8.95378 | |
| 0:00:02.572 32M / 8G INFO General (genomic_info_filler.cpp : 119) EC coverage threshold value was calculated as 8.95378 | |
| 0:00:02.572 32M / 8G INFO General (genomic_info_filler.cpp : 120) Trusted kmer low bound: 0 | |
| 0:00:02.572 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == Simplification | |
| 0:00:02.572 32M / 8G INFO General (graph_simplification.hpp : 970) Graph simplification started | |
| 0:00:02.572 32M / 8G INFO General (graph_simplification.hpp : 975) Fast simplification mode disabled | |
| 0:00:02.573 32M / 8G INFO General (graph_simplification.hpp : 695) PROCEDURE == Presimplification | |
| 0:00:02.573 32M / 8G INFO General (graph_simplification.hpp : 213) Removing short low covered self-conjugate connections | |
| 0:00:02.573 32M / 8G INFO General (graph_simplification.hpp : 699) Further presimplification is disabled | |
| 0:00:02.573 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 1 | |
| 0:00:02.575 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.581 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.663 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.663 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 2 | |
| 0:00:02.665 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.669 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.691 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.702 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 3 | |
| 0:00:02.703 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.705 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.741 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.744 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 4 | |
| 0:00:02.744 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.746 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.762 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.763 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 5 | |
| 0:00:02.764 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.765 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.772 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.773 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 6 | |
| 0:00:02.773 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.775 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.780 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.781 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 7 | |
| 0:00:02.781 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.783 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.788 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.789 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 8 | |
| 0:00:02.789 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.791 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.795 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.795 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 9 | |
| 0:00:02.796 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.797 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.800 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.801 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 10 | |
| 0:00:02.801 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.802 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.805 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.806 32M / 8G INFO General (graph_simplification.hpp : 839) PROCEDURE == Post simplification | |
| 0:00:02.806 32M / 8G INFO General (graph_simplification.hpp : 856) Iteration 0 | |
| 0:00:02.806 32M / 8G INFO General (graph_simplification.hpp : 290) Clipping tips based on topology | |
| 0:00:02.807 32M / 8G INFO General (graph_simplification.hpp : 255) Removal of relatively low covered connections disabled | |
| 0:00:02.807 32M / 8G INFO General (graph_simplification.hpp : 530) Complex tip clipping disabled | |
| 0:00:02.807 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.807 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.810 32M / 8G INFO General (graph_simplification.hpp : 856) Iteration 1 | |
| 0:00:02.810 32M / 8G INFO General (graph_simplification.hpp : 290) Clipping tips based on topology | |
| 0:00:02.811 32M / 8G INFO General (graph_simplification.hpp : 255) Removal of relatively low covered connections disabled | |
| 0:00:02.811 32M / 8G INFO General (graph_simplification.hpp : 530) Complex tip clipping disabled | |
| 0:00:02.811 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.811 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.812 32M / 8G INFO General (graph_simplification.hpp : 392) Removing hidden erroneous connections | |
| 0:00:02.813 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup | |
| 0:00:02.813 32M / 8G INFO General (graph_simplification.hpp : 406) Removing isolated edges | |
| 0:00:02.813 32M / 8G INFO General (graph_simplification.hpp : 407) All edges shorter than 150 will be removed | |
| 0:00:02.814 32M / 8G INFO General (graph_simplification.hpp : 408) Also edges shorter than 0 and coverage smaller than 2 will be removed | |
| 0:00:02.815 32M / 8G INFO General (simplification.cpp : 88) Counting average coverage | |
| 0:00:02.816 32M / 8G INFO General (simplification.cpp : 91) Average coverage = 1515.71 | |
| 0:00:02.816 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == Contig Output | |
| 0:00:02.816 32M / 8G INFO General (contig_output.hpp : 297) Outputting contigs to /scratch/users/yehang/individual/results/28625//K33/simplified_contigs.fasta | |
| 0:00:02.829 32M / 8G INFO General (contig_output.hpp : 297) Outputting contigs to /scratch/users/yehang/individual/results/28625//K33/before_rr.fasta | |
| 0:00:02.843 32M / 8G INFO General (contig_output.hpp : 334) Outputting graph to /scratch/users/yehang/individual/results/28625//K33/assembly_graph.fastg | |
| 0:00:02.867 32M / 8G INFO General (contig_output.hpp : 297) Outputting contigs to /scratch/users/yehang/individual/results/28625//K33/final_contigs.fasta | |
| 0:00:02.883 32M / 8G INFO General (launch.hpp : 112) SPAdes finished | |
| 0:00:02.887 32M / 8G INFO General (main.cpp : 168) Assembling time: 0 hours 0 minutes 2 seconds | |
| == Running assembler: K55 | |
| 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 43) Memory limit set to 64 Gb | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 147) Starting SPAdes, built from refs/heads/spades_3.6.2, git revision ed2c9d8f9dffb948d560432820a834bb60c8de8d | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 148) Assembling dataset (/scratch/users/yehang/individual/results/28625/dataset.info) with K=55 | |
| 0:00:00.000 4M / 4M INFO General (launch.hpp : 30) SPAdes started | |
| 0:00:00.000 4M / 4M INFO General (launch.hpp : 31) Starting from stage: construction | |
| 0:00:00.000 4M / 4M INFO General (launch.hpp : 39) Two-step RR enabled: 0 | |
| 0:00:00.001 4M / 4M INFO General (launch.hpp : 58) Will need read mapping, kmer mapper will be attached | |
| 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction | |
| 0:00:00.001 4M / 4M INFO General (construction.cpp : 45) Contigs from previous K will be used | |
| 0:00:00.003 4M / 4M INFO General (read_converter.hpp : 49) Binary reads detected | |
| 0:00:00.006 4M / 4M INFO General (graph_construction.hpp : 130) Constructing DeBruijn graph for k=55 | |
| 0:00:00.007 4M / 4M INFO General (kmer_splitters.hpp : 179) Splitting kmer instances into 64 buckets. This might take a while. | |
| 0:00:00.007 4M / 4M INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:00.007 4M / 4M INFO General (kmer_splitters.hpp : 197) Memory available for splitting buffers: 2.6665 Gb | |
| 0:00:00.007 4M / 4M INFO General (kmer_splitters.hpp : 206) Using cell size of 524288 | |
| 0:00:00.367 6G / 6G INFO General (kmer_splitters.hpp : 235) Processed 95662 reads | |
| 0:00:00.367 6G / 6G INFO General (kmer_splitters.hpp : 241) Adding contigs from previous K | |
| 0:00:00.451 6G / 6G INFO General (kmer_splitters.hpp : 252) Used 95662 reads. Maximum read length 150 | |
| 0:00:00.451 6G / 6G INFO General (kmer_splitters.hpp : 253) Average read length 110.578 | |
| 0:00:00.458 32M / 6G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:00.539 32M / 6G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 83769 kmers in total. | |
| 0:00:00.540 32M / 6G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:00.643 32M / 6G INFO K-mer Index Building (kmer_index.hpp : 464) Building kmer index | |
| 0:00:00.643 32M / 6G INFO General (kmer_splitters.hpp : 386) Splitting kmer instances into 128 buckets. This might take a while. | |
| 0:00:00.643 32M / 6G INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:00.643 32M / 6G INFO General (kmer_splitters.hpp : 404) Memory available for splitting buffers: 2.66536 Gb | |
| 0:00:00.643 32M / 6G INFO General (kmer_splitters.hpp : 412) Using cell size of 262144 | |
| 0:00:01.065 8G / 8G INFO General (kmer_splitters.hpp : 435) Processed 83769 kmers | |
| 0:00:01.065 8G / 8G INFO General (kmer_splitters.hpp : 444) Used 83769 kmers. | |
| 0:00:01.079 32M / 8G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:01.227 32M / 8G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 83734 kmers in total. | |
| 0:00:01.227 32M / 8G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:01.435 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 473) Building perfect hash indices | |
| 0:00:01.447 32M / 8G INFO General (kmer_index.hpp : 368) Merging final buckets. | |
| 0:00:01.484 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 521) Index built. Total 27480 bytes occupied (2.62546 bits per kmer). | |
| 0:00:01.484 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 391) Building k-mer extensions from k+1-mers | |
| 0:00:01.506 32M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index.hpp : 395) Building k-mer extensions from k+1-mers finished. | |
| 0:00:01.508 32M / 8G INFO General (graph_construction.hpp : 146) Condensing graph | |
| 0:00:01.508 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 338) Extracting unbranching paths | |
| 0:00:01.577 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 352) Extracting unbranching paths finished. 11772 sequences extracted | |
| 0:00:01.591 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 312) Collecting perfect loops | |
| 0:00:01.633 32M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 327) Collecting perfect loops finished. 2 loops collected | |
| 0:00:01.643 32M / 8G INFO General (graph_construction.hpp : 151) Building index with from graph | |
| 0:00:01.644 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 464) Building kmer index | |
| 0:00:01.644 32M / 8G INFO General (kmer_splitters.hpp : 296) Splitting kmer instances into 16 buckets. This might take a while. | |
| 0:00:01.644 32M / 8G INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:01.644 32M / 8G INFO General (kmer_splitters.hpp : 314) Memory available for splitting buffers: 21.3229 Gb | |
| 0:00:01.644 32M / 8G INFO General (kmer_splitters.hpp : 319) Using cell size of 2097152 | |
| 0:00:01.705 608M / 8G INFO General (kmer_splitters.hpp : 332) Processed 11774 edges | |
| 0:00:01.705 608M / 8G INFO General (kmer_splitters.hpp : 337) Used 11774 sequences. | |
| 0:00:01.705 32M / 8G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:01.789 32M / 8G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 83769 kmers in total. | |
| 0:00:01.789 32M / 8G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:01.836 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 473) Building perfect hash indices | |
| 0:00:01.892 32M / 8G INFO General (kmer_index.hpp : 368) Merging final buckets. | |
| 0:00:01.929 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 521) Index built. Total 27496 bytes occupied (2.62589 bits per kmer). | |
| 0:00:01.931 36M / 8G INFO General (edge_index_builders.hpp : 28) Collecting k-mer coverage information from graph, this takes a while. | |
| 0:00:02.054 36M / 8G INFO General (graph_construction.hpp : 183) Filling coverage index | |
| 0:00:02.054 36M / 8G INFO General (edge_index_builders.hpp : 106) Collecting k-mer coverage information from reads, this takes a while. | |
| 0:00:02.432 32M / 8G INFO General (graph_construction.hpp : 185) Filling coverage and flanking coverage from index | |
| 0:00:02.434 32M / 8G INFO General (construction.cpp : 34) Figured out: read length = 150 | |
| 0:00:02.437 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding | |
| 0:00:02.442 32M / 8G INFO ThresholdFinder (omni_tools.hpp : 304) Bucket size: 14 | |
| 0:00:02.442 32M / 8G INFO ThresholdFinder (omni_tools.hpp : 319) Proper threshold was not found. Threshold set to 0.1 of average coverage | |
| 0:00:02.443 32M / 8G INFO General (genomic_info_filler.cpp : 76) Average edge coverage: 32.0185 | |
| 0:00:02.443 32M / 8G INFO General (genomic_info_filler.cpp : 77) Graph threshold: 3.20185 | |
| 0:00:02.447 32M / 8G INFO General (genomic_info_filler.cpp : 119) EC coverage threshold value was calculated as 3.20185 | |
| 0:00:02.447 32M / 8G INFO General (genomic_info_filler.cpp : 120) Trusted kmer low bound: 0 | |
| 0:00:02.447 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer | |
| 0:00:02.449 32M / 8G INFO General (gap_closer.cpp : 165) Preparing shift maps | |
| 0:00:02.453 36M / 8G INFO General (gap_closer.cpp : 125) Processing paired reads (takes a while) | |
| 0:00:02.630 36M / 8G INFO General (gap_closer.cpp : 144) Used 46916 paired reads | |
| 0:00:02.630 36M / 8G INFO General (gap_closer.cpp : 146) Merging paired indices | |
| 0:00:02.632 36M / 8G INFO GapCloser (gap_closer.cpp : 403) Closing short gaps | |
| 0:00:02.642 36M / 8G INFO GapCloser (gap_closer.cpp : 432) Closing short gaps complete: filled 0 gaps after checking 16 candidates | |
| 0:00:02.645 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == Simplification | |
| 0:00:02.646 32M / 8G INFO General (graph_simplification.hpp : 970) Graph simplification started | |
| 0:00:02.646 32M / 8G INFO General (graph_simplification.hpp : 975) Fast simplification mode disabled | |
| 0:00:02.646 32M / 8G INFO General (graph_simplification.hpp : 695) PROCEDURE == Presimplification | |
| 0:00:02.646 32M / 8G INFO General (graph_simplification.hpp : 213) Removing short low covered self-conjugate connections | |
| 0:00:02.647 32M / 8G INFO General (graph_simplification.hpp : 699) Further presimplification is disabled | |
| 0:00:02.647 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 1 | |
| 0:00:02.651 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.678 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.715 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.716 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 2 | |
| 0:00:02.717 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.721 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.740 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.740 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 3 | |
| 0:00:02.742 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.746 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.764 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.765 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 4 | |
| 0:00:02.766 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.770 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.789 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.798 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 5 | |
| 0:00:02.799 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.802 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.860 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.862 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 6 | |
| 0:00:02.863 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.865 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.880 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.882 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 7 | |
| 0:00:02.883 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.885 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.898 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.899 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 8 | |
| 0:00:02.900 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.902 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.918 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.919 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 9 | |
| 0:00:02.920 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.922 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.932 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.933 32M / 8G INFO General (graph_simplification.hpp : 925) PROCEDURE == Simplification cycle, iteration 10 | |
| 0:00:02.934 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.936 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.944 32M / 8G INFO General (graph_simplification.hpp : 190) Removing low covered connections | |
| 0:00:02.945 32M / 8G INFO General (graph_simplification.hpp : 839) PROCEDURE == Post simplification | |
| 0:00:02.945 32M / 8G INFO General (graph_simplification.hpp : 856) Iteration 0 | |
| 0:00:02.945 32M / 8G INFO General (graph_simplification.hpp : 290) Clipping tips based on topology | |
| 0:00:02.947 32M / 8G INFO General (graph_simplification.hpp : 255) Removal of relatively low covered connections disabled | |
| 0:00:02.947 32M / 8G INFO General (graph_simplification.hpp : 275) Removing connections based on topology | |
| 0:00:02.950 32M / 8G INFO General (graph_simplification.hpp : 340) Removing connections based on topology and reliable coverage | |
| 0:00:02.951 32M / 8G INFO General (graph_simplification.hpp : 324) Removing interstrand connections | |
| 0:00:02.959 32M / 8G INFO General (graph_simplification.hpp : 308) Removing connections based on topological multiplicity counting | |
| 0:00:02.963 32M / 8G INFO General (graph_simplification.hpp : 530) Complex tip clipping disabled | |
| 0:00:02.963 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.965 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.972 32M / 8G INFO General (graph_simplification.hpp : 856) Iteration 1 | |
| 0:00:02.972 32M / 8G INFO General (graph_simplification.hpp : 290) Clipping tips based on topology | |
| 0:00:02.974 32M / 8G INFO General (graph_simplification.hpp : 255) Removal of relatively low covered connections disabled | |
| 0:00:02.974 32M / 8G INFO General (graph_simplification.hpp : 275) Removing connections based on topology | |
| 0:00:02.976 32M / 8G INFO General (graph_simplification.hpp : 340) Removing connections based on topology and reliable coverage | |
| 0:00:02.978 32M / 8G INFO General (graph_simplification.hpp : 324) Removing interstrand connections | |
| 0:00:02.981 32M / 8G INFO General (graph_simplification.hpp : 308) Removing connections based on topological multiplicity counting | |
| 0:00:02.984 32M / 8G INFO General (graph_simplification.hpp : 530) Complex tip clipping disabled | |
| 0:00:02.985 32M / 8G INFO General (graph_simplification.hpp : 96) Clipping tips | |
| 0:00:02.987 32M / 8G INFO General (graph_simplification.hpp : 150) Removing bulges | |
| 0:00:02.990 32M / 8G INFO General (graph_simplification.hpp : 392) Removing hidden erroneous connections | |
| 0:00:02.992 32M / 8G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer | |
| 0:00:02.992 32M / 8G INFO General (graph_pack.hpp : 85) Index refill | |
| 0:00:02.993 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 464) Building kmer index | |
| 0:00:02.993 32M / 8G INFO General (kmer_splitters.hpp : 296) Splitting kmer instances into 16 buckets. This might take a while. | |
| 0:00:02.993 32M / 8G INFO General (file_limit.hpp : 30) Open file limit set to 65536 | |
| 0:00:02.993 32M / 8G INFO General (kmer_splitters.hpp : 314) Memory available for splitting buffers: 21.3229 Gb | |
| 0:00:02.993 32M / 8G INFO General (kmer_splitters.hpp : 319) Using cell size of 2097152 | |
| 0:00:03.035 608M / 8G INFO General (kmer_splitters.hpp : 332) Processed 2118 edges | |
| 0:00:03.035 608M / 8G INFO General (kmer_splitters.hpp : 337) Used 2118 sequences. | |
| 0:00:03.035 32M / 8G INFO General (kmer_index.hpp : 342) Starting k-mer counting. | |
| 0:00:03.099 32M / 8G INFO General (kmer_index.hpp : 348) K-mer counting done. There are 28420 kmers in total. | |
| 0:00:03.099 32M / 8G INFO General (kmer_index.hpp : 350) Merging temporary buckets. | |
| 0:00:03.153 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 473) Building perfect hash indices | |
| 0:00:03.182 32M / 8G INFO General (kmer_index.hpp : 368) Merging final buckets. | |
| 0:00:03.211 32M / 8G INFO K-mer Index Building (kmer_index.hpp : 521) Index built. Total 9448 bytes occupied (2.65954 bits per kmer). | |
| 0:00:03.212 36M / 8G INFO General (edge_index_builders.hpp : 28) Collecting k-mer coverage information from graph, this takes a while. | |
| 0:00:03.251 36M / 8G INFO General (gap_closer.cpp : 165) Preparing shift maps | |
| 0:00:03.252 36M / 8G INFO General (gap_closer.cpp : 125) Processing paired reads (takes a while) | |
| 0:00:03.407 36M / 8G INFO General (gap_closer.cpp : 144) Used 46916 paired reads | |
| 0:00:03.407 36M / 8G INFO General (gap_closer.cpp : 146) Merging paired indices | |
| 0:00:03.408 36M / 8G INFO GapCloser (gap_closer.cpp : 403) Closing short gaps | |
| 0:00:03.409 36M / 8G INFO GapCloser (gap_closer.cpp : 432) Closing short gaps complete: filled 0 gaps after checking 0 candidates | |
| 0:00:03.411 36M / 8G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup | |
| 0:00:03.412 36M / 8G INFO General (graph_simplification.hpp : 406) Removing isolated edges | |
| 0:00:03.412 36M / 8G INFO General (graph_simplification.hpp : 407) All edges shorter than 150 will be removed | |
| 0:00:03.412 36M / 8G INFO General (graph_simplification.hpp : 408) Also edges shorter than 0 and coverage smaller than 2 will be removed | |
| 0:00:03.445 36M / 8G INFO General (simplification.cpp : 88) Counting average coverage | |
| 0:00:03.445 36M / 8G INFO General (simplification.cpp : 91) Average coverage = 412.852 | |
| 0:00:03.445 36M / 8G INFO StageManager (stage.cpp : 126) STAGE == Mismatch Correction | |
| 0:00:03.661 36M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions | |
| 0:00:03.669 36M / 8G INFO General (mismatch_shall_not_pass.hp: 292) All edges processed | |
| 0:00:03.670 36M / 8G INFO General (mismatch_correction.cpp : 19) Corrected 0 nucleotides | |
| 0:00:03.672 36M / 8G INFO StageManager (stage.cpp : 126) STAGE == Paired Information Counting | |
| 0:00:03.674 36M / 8G INFO General (pair_info_count.cpp : 166) Min edge length for estimation: 35 | |
| 0:00:03.674 36M / 8G INFO General (pair_info_count.cpp : 168) Estimating insert size for library #0 | |
| 0:00:03.674 36M / 8G INFO General (pair_info_count.cpp : 32) Estimating insert size (takes a while) | |
| 0:00:03.676 36M / 8G INFO General (short_read_mapper.hpp : 93) Selecting usual mapper | |
| 0:00:03.755 36M / 8G INFO General (sequence_mapper_notifier.h: 90) Processed 23458 reads | |
| 0:00:03.755 36M / 8G INFO General (pair_info_count.cpp : 43) 4 paired reads (0.0170518% of all) aligned to long edges | |
| 0:00:03.756 36M / 8G INFO General (pair_info_count.cpp : 186) Estimated insert size for paired library #0 | |
| 0:00:03.756 36M / 8G INFO General (pair_info_count.cpp : 191) Insert size = 57, deviation = 0, left quantile = 57, right quantile = 57, read length = 150 | |
| 0:00:03.756 36M / 8G INFO General (pair_info_count.cpp : 197) Mapping library #0 | |
| 0:00:03.756 36M / 8G INFO General (pair_info_count.cpp : 207) Mapping paired reads (takes a while) | |
| 0:00:03.756 36M / 8G INFO General (pair_info_count.cpp : 84) Left insert size qauntile 57, right insert size quantile 57 | |
| 0:00:03.758 36M / 8G INFO General (short_read_mapper.hpp : 93) Selecting usual mapper | |
| 0:00:09.685 116M / 8G INFO General (sequence_mapper_notifier.h: 82) Processed 35188 reads | |
| 0:00:12.461 92M / 8G INFO General (sequence_mapper_notifier.h: 90) Processed 46916 reads | |
| 0:00:12.461 92M / 8G INFO General (split_graph_pair_info.hpp : 351) Threshold for paired information inf | |
| 0:00:12.461 92M / 8G INFO General (short_read_mapper.hpp : 93) Selecting usual mapper | |
| 0:00:12.578 84M / 8G INFO General (sequence_mapper_notifier.h: 82) Processed 35874 reads | |
| 0:00:12.590 84M / 8G INFO General (sequence_mapper_notifier.h: 90) Processed 47831 reads | |
| 0:00:12.610 80M / 8G INFO General (pair_info_count.cpp : 215) Total paths obtained from single reads: 5532 | |
| 0:00:12.610 80M / 8G INFO StageManager (stage.cpp : 126) STAGE == Distance Estimation | |
| 0:00:12.610 80M / 8G INFO General (distance_estimation.cpp : 235) Processing library #0 | |
| 0:00:12.610 80M / 8G INFO General (distance_estimation.cpp : 137) Weight Filter Done | |
| 0:00:12.610 80M / 8G INFO DistanceEstimator (distance_estimation.hpp : 188) Using SIMPLE distance estimator | |
| === Stack Trace === | |
| === Stack Trace === | |
| === Stack Trace === | |
| === Stack Trace === | |
| === Stack Trace === | |
| === Stack Trace === | |
| === Stack Trace === | |
| === Stack Trace === | |
| [0x405b7a] | |
| [0x567eaa] | |
| [0x589568] | |
| [0x58a41a] | |
| [0x566607] | |
| [0x7aa829] | |
| [0x7b2f2d] | |
| [0x7f2aa9] | |
| spades: /home/yasha/gitrep3/algorithmic-biology/assembler/src/include/omni/omni_utils.hpp:575: size_t omnigraph::PairInfoPathLengthUpperBound(size_t, size_t, double): Assertion `math::gr(answer, 0.)' failed. | |
| == Error == system call for: "['/cm/shared/c3ddb/SPAdes/3.6.2/bin/spades', '/scratch/users/yehang/individual/results/28625/K55/configs/config.info']" finished abnormally, err code: -6 | |
| In case you have troubles running SPAdes, you can write to [email protected] | |
| Please provide us with params.txt and spades.log files from the output directory. |
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