I try to perform a hybrid assembly using Unicycler. Unicycler use SPAdes to assembly the illumina sequences, and the program crashes while in SPAdes. The spades.log file says something about an invalid argument and error code 22. I have run the spades.py --test, and everything seems to work fine.
Command line: /home/user/SPAdes-3.11.1-Linux/bin/spades.py -1 /home/user/minion/organism/Illumina/BD_S3_L001_R1_001.fastq.gz -2 /home/user/minion/organism/Illumina/BD_S3_L001_R2_001.fastq.gz -o /home/user/minion/organism/hybrid_assembly/spades_assembly/read_correction --threads 8 --only-error-correction
System information:
SPAdes version: 3.11.1
Python version: 2.7.12
OS: Linux-4.10.0-40-generic-x86_64-with-Ubuntu-16.04-xenial
Output dir: /home/user/minion/organism/hybrid_assembly/spades_assembly/read_correction
Mode: ONLY read error correction (without 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/user/minion/organism/Illumina/BD_S3_L001_R1_001.fastq.gz']
right reads: ['/home/user/minion/organism/Illumina/BD_S3_L001_R2_001.fastq.gz']
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)
Other parameters:
Dir for temp files: /home/user/minion/organism/hybrid_assembly/spades_assembly/read_correction/tmp
Threads: 8
Memory limit (in Gb): 87
======= SPAdes pipeline started. Log can be found here: /home/user/minion/organism/hybrid_assembly/spades_assembly/read_correction/spades.log
===== Read error correction started.
== Running read error correction tool: /home/user/SPAdes-3.11.1-Linux/bin/hammer /home/user/minion/organism/hybrid_assembly/spades_assembly/read_correction/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
0:00:00.001 4M / 4M INFO General (main.cpp : 84) Loading config from /home/user/minion/organism/hybrid_assembly/spades_assembly/read_correction/corrected/configs/config.info
0:00:00.045 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 87 Gb
0:00:00.045 4M / 4M INFO General (main.cpp : 93) Trying to determine PHRED offset
0:00:00.071 4M / 4M INFO General (main.cpp : 99) Determined value is 33
0:00:00.071 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.072 4M / 4M INFO General (main.cpp : 120) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.100 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:00.101 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 128 buckets using 8 threads. This might take a while.
0:00:00.101 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:00.101 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.62484 Gb
0:00:00.101 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 524288
0:00:00.102 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 96) Processing /home/user/minion/organism/Illumina/BD_S3_L001_R1_001.fastq.gz
0:00:57.279 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 1338594 reads
0:03:30.505 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 2152556 reads
0:03:30.505 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 96) Processing /home/user/minion/organism/Illumina/BD_S3_L001_R2_001.fastq.gz
0:09:23.290 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 3442412 reads
0:14:08.692 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 4305112 reads
0:14:08.692 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 111) Total 4305112 reads processed
0:14:08.726 32M / 8G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:20:36.408 32M / 8G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 205776690 kmers in total.
0:20:36.409 32M / 8G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:24:43.505 32M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:25:40.125 100M / 8G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
1:11:46.553 100M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 95426752 bytes occupied (3.70991 bits per kmer).
1:11:46.598 100M / 8G INFO K-mer Counting (kmer_data.cpp : 357) Arranging kmers in hash map order
1:12:55.597 3G / 8G INFO General (main.cpp : 155) Clustering Hamming graph.
1:21:35.596 3G / 8G INFO General (main.cpp : 162) Extracting clusters
=== Stack Trace ===
[0x407a6a]
[0x409561]
[0x40c79b]
[0x40129a]
[0x5442b0]
[0x40620d]
Verification of expression '(intptr_t) MappedRegion != -1L' failed in function 'void MMappedWriter::reserve(size_t)'. In file '/spades/src/common/io/kmers/mmapped_writer.hpp' on line 94. Message 'mmap(2) failed. Reason: Invalid argument. Error code: 22'.
Verification of expression '(intptr_t) MappedRegion != -1L' failed in function 'void MMappedWriter::reserve(size_t)'. In file '/spades/src/common/io/kmers/mmapped_writer.hpp' on line 94. Message 'mmap(2) failed. Reason: Invalid argument. Error code: 22'.
hammer: /spades/src/common/io/kmers/mmapped_writer.hpp:94: void MMappedWriter::reserve(size_t): Assertion `(intptr_t) MappedRegion != -1L' failed.
== Error == system call for: "['/home/user/SPAdes-3.11.1-Linux/bin/hammer', '/home/user/minion/organism/hybrid_assembly/spades_assembly/read_correction/corrected/configs/config.info']" finished abnormally, err code: -6
In case you have troubles running SPAdes, you can write to [email protected]
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.
