Created
September 15, 2017 22:40
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| Command line: /Users/olgabot/anaconda3/envs/winky/bin/spades.py --12 /Users/olgabot/code/winky/winky/test/data/ZN-1-concatenated.fastq -o /Users/olgabot/code/winky/notebooks/spades-ZN-1 | |
| System information: | |
| SPAdes version: 3.11.0 | |
| Python version: 3.5.2 | |
| OS: Darwin-16.7.0-x86_64-i386-64bit | |
| Output dir: /Users/olgabot/code/winky/notebooks/spades-ZN-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: not specified | |
| right reads: not specified | |
| interlaced reads: ['/Users/olgabot/code/winky/winky/test/data/ZN-1-concatenated.fastq'] | |
| 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: 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: /Users/olgabot/code/winky/notebooks/spades-ZN-1/tmp | |
| Threads: 16 | |
| Memory limit (in Gb): 250 | |
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| Command line: /Users/olgabot/anaconda3/envs/winky/bin/spades.py --12 /Users/olgabot/code/winky/winky/test/data/ZN-1-concatenated.fastq -o /Users/olgabot/code/winky/notebooks/spades-ZN-1 | |
| System information: | |
| SPAdes version: 3.11.0 | |
| Python version: 3.5.2 | |
| OS: Darwin-16.7.0-x86_64-i386-64bit | |
| Output dir: /Users/olgabot/code/winky/notebooks/spades-ZN-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: not specified | |
| right reads: not specified | |
| interlaced reads: ['/Users/olgabot/code/winky/winky/test/data/ZN-1-concatenated.fastq'] | |
| 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: 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: /Users/olgabot/code/winky/notebooks/spades-ZN-1/tmp | |
| Threads: 16 | |
| Memory limit (in Gb): 250 | |
| ======= SPAdes pipeline started. Log can be found here: /Users/olgabot/code/winky/notebooks/spades-ZN-1/spades.log | |
| == Splitting /Users/olgabot/code/winky/winky/test/data/ZN-1-concatenated.fastq into left and right reads (in /Users/olgabot/code/winky/notebooks/spades-ZN-1/split_input directory) | |
| ===== Read error correction started. | |
| == Running read error correction tool: /Users/olgabot/anaconda3/envs/winky/share/spades-3.11.0-0/bin/hammer /Users/olgabot/code/winky/notebooks/spades-ZN-1/corrected/configs/config.info | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 83) Starting BayesHammer, built from N/A, git revision N/A | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Loading config from /Users/olgabot/code/winky/notebooks/spades-ZN-1/corrected/configs/config.info | |
| 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 250 Gb | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 93) Trying to determine PHRED offset | |
| 0:00:00.002 4M / 4M INFO General (main.cpp : 99) Determined value is 33 | |
| 0:00:00.002 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] | |
| 0:00:00.002 4M / 4M INFO General (main.cpp : 120) Size of aux. kmer data 24 bytes | |
| === ITERATION 0 begins === | |
| 0:00:00.002 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index | |
| 0:00:00.002 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 1 threads. This might take a while. | |
| 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 256 | |
| 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 83.332 Gb | |
| 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 4194304 | |
| 0:00:00.002 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 96) Processing /Users/olgabot/code/winky/notebooks/spades-ZN-1/split_input/ZN-1-concatenated_1.fastq | |
| 0:00:00.010 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 96) Processing /Users/olgabot/code/winky/notebooks/spades-ZN-1/split_input/ZN-1-concatenated_2.fastq | |
| 0:00:00.012 580M / 616M INFO K-mer Splitting (kmer_data.cpp : 111) Total 4 reads processed | |
| 0:00:00.012 4M / 616M INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. | |
| 0:00:00.022 4M / 616M INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 5214 kmers in total. | |
| 0:00:00.022 4M / 616M INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. | |
| 0:00:00.026 4M / 616M INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices | |
| 0:00:00.054 4M / 616M INFO General (kmer_index_builder.hpp : 137) Merging final buckets. | |
| 0:00:00.056 4M / 616M INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 11512 bytes occupied (17.6632 bits per kmer). | |
| 0:00:00.056 4M / 616M INFO K-mer Counting (kmer_data.cpp : 357) Arranging kmers in hash map order | |
| 0:00:00.056 4M / 616M INFO General (main.cpp : 155) Clustering Hamming graph. | |
| 0:00:00.072 4M / 616M INFO General (main.cpp : 162) Extracting clusters | |
| 0:00:00.074 4M / 616M INFO General (main.cpp : 174) Clustering done. Total clusters: 5194 | |
| 0:00:00.074 4M / 616M INFO K-mer Counting (kmer_data.cpp : 379) Collecting K-mer information, this takes a while. | |
| 0:00:00.074 4M / 616M INFO K-mer Counting (kmer_data.cpp : 385) Processing /Users/olgabot/code/winky/notebooks/spades-ZN-1/split_input/ZN-1-concatenated_1.fastq | |
| 0:00:00.075 4M / 616M INFO K-mer Counting (kmer_data.cpp : 385) Processing /Users/olgabot/code/winky/notebooks/spades-ZN-1/split_input/ZN-1-concatenated_2.fastq | |
| 0:00:00.076 4M / 616M INFO K-mer Counting (kmer_data.cpp : 392) Collection done, postprocessing. | |
| 0:00:00.076 4M / 616M INFO K-mer Counting (kmer_data.cpp : 406) There are 5214 kmers in total. Among them 3374 (64.7104%) are singletons. | |
| 0:00:00.076 4M / 616M INFO General (main.cpp : 180) Subclustering Hamming graph | |
| 0:00:00.078 4M / 616M INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. | |
| 0:00:00.078 4M / 616M INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: | |
| 0:00:00.078 4M / 616M INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 5174. Among them 4208 (81.3297%) are good | |
| 0:00:00.078 4M / 616M INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 0. Among them 0 (nan%) are good | |
| 0:00:00.078 4M / 616M INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 20. Among them 0 (0%) are good | |
| 0:00:00.078 4M / 616M INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2 kmers | |
| 0:00:00.078 4M / 616M INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1 | |
| 0:00:00.078 4M / 616M INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 4208 | |
| 0:00:00.078 4M / 616M INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.971698,0.0188679,0.00943396,0),(0,0.932692,0.0384615,0.0288462),(0.0283019,0.0377358,0.915094,0.0188679),(0,0.00961538,0,0.990385)) | |
| 0:00:00.078 4M / 616M INFO General (main.cpp : 185) Finished clustering. | |
| 0:00:00.078 4M / 616M INFO General (main.cpp : 204) Starting solid k-mers expansion in 1 threads. | |
| 0:00:00.078 4M / 616M INFO General (main.cpp : 225) Solid k-mers iteration 0 produced 0 new k-mers. | |
| 0:00:00.078 4M / 616M INFO General (main.cpp : 229) Solid k-mers finalized | |
| 0:00:00.078 4M / 616M INFO General (hammer_tools.cpp : 211) Starting read correction in 1 threads. | |
| 0:00:00.078 4M / 616M INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /Users/olgabot/code/winky/notebooks/spades-ZN-1/split_input/ZN-1-concatenated_1.fastq and /Users/olgabot/code/winky/notebooks/spades-ZN-1/split_input/ZN-1-concatenated_2.fastq | |
| 0:00:00.087 28M / 616M INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 2 reads. | |
| 0:00:00.088 28M / 616M INFO General (hammer_tools.cpp : 175) Processed batch 0 | |
| 0:00:00.088 28M / 616M INFO General (hammer_tools.cpp : 185) Written batch 0 | |
| 0:00:00.092 4M / 616M INFO General (hammer_tools.cpp : 270) Correction done. Changed 0 bases in 0 reads. | |
| 0:00:00.092 4M / 616M INFO General (hammer_tools.cpp : 271) Failed to correct 0 bases out of 3824. | |
| 0:00:00.092 4M / 616M INFO General (main.cpp : 255) Too few reads have changed in this iteration. Exiting. | |
| 0:00:00.092 4M / 616M INFO General (main.cpp : 262) Saving corrected dataset description to /Users/olgabot/code/winky/notebooks/spades-ZN-1/corrected/corrected.yaml | |
| 0:00:00.093 4M / 616M INFO General (main.cpp : 269) All done. Exiting. | |
| == Compressing corrected reads (with gzip) | |
| == Dataset description file was created: /Users/olgabot/code/winky/notebooks/spades-ZN-1/corrected/corrected.yaml | |
| ===== Read error correction finished. | |
| ===== Assembling started. | |
| == Running assembler: K21 | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /Users/olgabot/code/winky/notebooks/spades-ZN-1/K21/configs/config.info | |
| 0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 250 Gb | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128 | |
| 0:00:00.000 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/Users/olgabot/code/winky/notebooks/spades-ZN-1/dataset.info) with K=21 | |
| 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 : 61) Two-step RR enabled: 0 | |
| 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction | |
| 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 84) Converting reads to binary format for library #0 (takes a while) | |
| 0:00:00.000 4M / 4M INFO General (read_converter.hpp : 85) Converting paired reads | |
| 0:00:00.122 68M / 132M INFO General (binary_converter.hpp : 159) 2 reads written | |
| 0:00:00.127 4M / 132M INFO General (read_converter.hpp : 94) Converting single reads | |
| 0:00:00.360 132M / 260M INFO General (binary_converter.hpp : 159) 0 reads written | |
| 0:00:00.375 4M / 260M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=21 | |
| 0:00:00.376 4M / 260M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 1 buckets using 1 threads. This might take a while. | |
| 0:00:00.376 4M / 260M INFO General (file_limit.hpp : 32) Open file limit set to 256 | |
| 0:00:00.377 4M / 260M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 83.332 Gb | |
| 0:00:00.377 4M / 260M INFO General (kmer_splitters.hpp : 82) Using cell size of 67108864 | |
| 0:00:00.379 568M / 1G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K | |
| 0:00:00.379 4M / 1G INFO General (kmer_splitters.hpp : 310) Used 8 reads. Maximum read length 985 | |
| 0:00:00.379 4M / 1G INFO General (kmer_splitters.hpp : 311) Average read length 956 | |
| 0:00:00.379 4M / 1G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. | |
| 0:00:00.381 4M / 1G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 2607 kmers in total. | |
| 0:00:00.381 4M / 1G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. | |
| 0:00:00.381 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index | |
| 0:00:00.381 4M / 1G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 1 threads. This might take a while. | |
| 0:00:00.381 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 256 | |
| 0:00:00.381 4M / 1G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 83.332 Gb | |
| 0:00:00.381 4M / 1G INFO General (kmer_splitters.hpp : 82) Using cell size of 4194304 | |
| 0:00:00.386 580M / 1G INFO General (kmer_splitters.hpp : 381) Processed 2607 kmers | |
| 0:00:00.386 580M / 1G INFO General (kmer_splitters.hpp : 386) Used 2607 kmers. | |
| 0:00:00.387 4M / 1G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. | |
| 0:00:00.394 4M / 1G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 2607 kmers in total. | |
| 0:00:00.394 4M / 1G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. | |
| 0:00:00.397 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices | |
| 0:00:00.421 4M / 1G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. | |
| 0:00:00.423 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 10368 bytes occupied (31.8159 bits per kmer). | |
| 0:00:00.423 4M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers | |
| 0:00:00.424 4M / 1G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished. | |
| 0:00:00.424 4M / 1G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping | |
| 0:00:00.426 4M / 1G INFO Early tip clipping (early_simplification.hpp : 184) 59 22-mers were removed by early tip clipper | |
| 0:00:00.426 4M / 1G INFO General (graph_construction.hpp : 136) Condensing graph | |
| 0:00:00.426 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths | |
| 0:00:00.428 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted | |
| 0:00:00.429 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops | |
| 0:00:00.429 4M / 1G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected | |
| 0:00:00.429 4M / 1G INFO General (graph_construction.hpp : 141) Building index with from graph | |
| 0:00:00.430 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index | |
| 0:00:00.430 4M / 1G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 16 buckets using 1 threads. This might take a while. | |
| 0:00:00.430 4M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 256 | |
| 0:00:00.430 4M / 1G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 83.332 Gb | |
| 0:00:00.430 4M / 1G INFO General (kmer_splitters.hpp : 82) Using cell size of 4194304 | |
| 0:00:00.434 580M / 1G INFO General (edge_index_builders.hpp : 80) Used 8 sequences. | |
| 0:00:00.434 4M / 1G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting. | |
| 0:00:00.442 4M / 1G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 2548 kmers in total. | |
| 0:00:00.442 4M / 1G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets. | |
| 0:00:00.445 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices | |
| 0:00:00.467 4M / 1G INFO General (kmer_index_builder.hpp : 137) Merging final buckets. | |
| 0:00:00.469 4M / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 10352 bytes occupied (32.5024 bits per kmer). | |
| 0:00:00.469 4M / 1G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while. | |
| 0:00:00.469 4M / 1G INFO General (edge_index.hpp : 91) Index refilled | |
| 0:00:00.470 4M / 1G INFO General (graph_construction.hpp : 173) Filling coverage index | |
| 0:00:00.470 4M / 1G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while. | |
| 0:00:00.470 4M / 1G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index | |
| 0:00:00.470 4M / 1G INFO General (construction.cpp : 30) Figured out: read length = 985 | |
| 0:00:00.471 4M / 1G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding | |
| === Stack Trace === | |
| 0 spades 0x0000000107d4ed6d _ZN5utils16print_stacktraceEv + 173 | |
| 1 spades 0x0000000107fb6298 _ZN14coverage_model17KMerCoverageModel3FitEv + 328 | |
| 2 spades 0x0000000107f7d48b _ZN14debruijn_graph17GenomicInfoFiller3runERNS_10graph_packINS_13DeBruijnGraphEEEPKc + 1947 | |
| 3 spades 0x0000000107f49ff3 _ZN6spades12StageManager3runERN14debruijn_graph10graph_packINS1_13DeBruijnGraphEEEPKc + 931 | |
| 4 spades 0x0000000107d4c0ab _ZN6spades15assemble_genomeEv + 7531 | |
| 5 spades 0x0000000107d4dbbe main + 2894 | |
| 6 libdyld.dylib 0x00007fff9591c235 start + 1 | |
| 7 ??? 0x0000000000000002 0x0 + 2 | |
| Verification of expression 'cov_.size() > 10' failed in function 'void coverage_model::KMerCoverageModel::Fit()'. In file '/anaconda/conda-bld/spades_1505345597413/work/SPAdes-3.11.0/src/common/modules/coverage_model/kmer_coverage_model.cpp' on line 187. Message 'Invalid kmer coverage histogram, make sure that the coverage is indeed uniform'. | |
| Verification of expression 'cov_.size() > 10' failed in function 'void coverage_model::KMerCoverageModel::Fit()'. In file '/anaconda/conda-bld/spades_1505345597413/work/SPAdes-3.11.0/src/common/modules/coverage_model/kmer_coverage_model.cpp' on line 187. Message 'Invalid kmer coverage histogram, make sure that the coverage is indeed uniform'. | |
| Assertion failed: (cov_.size() > 10), function Fit, file /anaconda/conda-bld/spades_1505345597413/work/SPAdes-3.11.0/src/common/modules/coverage_model/kmer_coverage_model.cpp, line 187. | |
| == Error == system call for: "['/Users/olgabot/anaconda3/envs/winky/share/spades-3.11.0-0/bin/spades', '/Users/olgabot/code/winky/notebooks/spades-ZN-1/K21/configs/config.info']" finished abnormally, err code: -6 | |
| In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru | |
| or report an issue on our GitHub repository github.com/ablab/spades | |
| Please provide us with params.txt and spades.log files from the output directory. |
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