Hello, I am Using SPAdes for denovo assembly but I get this error what could be the reason, please!
below is the spade.log message!
Thank you.
Command line: /Users/eliasbalimponya/Applications/SPAdes/SPAdes-3.12.0-Darwin/bin/spades.py -m 750 -t 16 -k 55 -1 /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_1.fq -2 /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_2.fq -o /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_New
System information: SPAdes version: 3.12.0 Python version: 3.8.5 OS: macOS-10.16-x86_64-i386-64bit
Output dir: /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_New 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: ['/Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_1.fq'] right reads: ['/Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_2.fq'] 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: [55] 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/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_New/tmp Threads: 16 Memory limit (in Gb): 750
======= SPAdes pipeline started. Log can be found here: /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_New/spades.log
===== Read error correction started.
== Running read error correction tool: /Users/eliasbalimponya/Applications/SPAdes/SPAdes-3.12.0-Darwin/bin/spades-hammer /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_New/corrected/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_New/corrected/configs/config.info 0:00:00.002 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 8 0:00:00.002 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 750 Gb 0:00:00.002 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.003 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.003 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.003 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.003 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.003 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while. 0:00:00.003 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 256 0:00:00.003 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 31.2498 Gb 0:00:00.003 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 524288 0:00:00.004 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_1.fq 0:00:02.250 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 268685 reads 0:00:04.230 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 530715 reads 0:00:06.274 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 796008 reads 0:00:08.408 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1081531 reads 0:00:10.790 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1409615 reads 0:00:17.143 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 2290270 reads 0:00:18.138 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 2408256 reads 0:00:18.138 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_2.fq 0:00:36.974 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 4816512 reads 0:00:36.974 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4816512 reads processed 0:00:37.120 32M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:57.297 32M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 511363888 kmers in total. 0:00:57.297 32M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:59.415 32M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:01:25.103 256M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:01:27.225 256M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 237128440 bytes occupied (3.70974 bits per kmer). 0:01:27.226 256M / 8G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:01:56.159 7G / 8G INFO General (main.cpp : 148) Clustering Hamming graph. 0:17:11.344 7G / 8G INFO General (main.cpp : 155) Extracting clusters 4:59:34.945 7G / 25G INFO General (main.cpp : 167) Clustering done. Total clusters: 364945510 4:59:35.310 4G / 25G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 4:59:39.055 15G / 25G INFO K-mer Counting (kmer_data.cpp : 382) Processing /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_1.fq 8:34:17.562 15G / 25G INFO K-mer Counting (kmer_data.cpp : 382) Processing /Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_2.fq 20:56:39.662 15G / 25G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 21:13:52.123 15G / 25G INFO K-mer Counting (kmer_data.cpp : 403) There are 511363888 kmers in total. Among them 436528468 (85.3655%) are singletons. 21:13:52.123 15G / 25G INFO General (main.cpp : 173) Subclustering Hamming graph === Stack Trace === 0 spades-hammer 0x000000010248af63 _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEElNS0_5__ops15_Iter_comp_iterI23KMerStatCountComparatorEEEvT_SB_T0_T1_ + 2739 Assertion failed: (is.good()), function process, file /Users/asl/Temp/SPAdes-3.12.0/src/projects/hammer/kmer_cluster.cpp, line 620.
== Error == system call for: "['/Users/eliasbalimponya/Applications/SPAdes/SPAdes-3.12.0-Darwin/bin/spades-hammer', '/Users/eliasbalimponya/Documents/MIYAZAKI/NGS_PARENTS/Parent_New/corrected/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.
