finished abnormally, OS return value: -6

[Riverfishstar]

Description of bug

Hello, after I ran spades.py --careful -1 fastq/SRR21726401_1.fastq -2 fastq/SRR21726401_2.fastq -o out/3/ It occurred: spades-hammer: /spades/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:297: size_t kmers::KMerDiskCounter<Seq, traits>::MergeKMers(const string&, const string&) [with Seq = Seq<21>; traits = kmers::kmer_index_traits<Seq<21> >; size_t = long unsigned int; std::string = std::basic_string]: Assertion `std::is_sorted(beg, end, adt::array_less<typename Seq::DataType>())' failed. And: == Error == system call for: "['/home/zhening/Downloads/SPAdes-3.15.4-Linux/bin/spades-hammer', '/media/HDD_3/hyx/phage_design/Bacterial_sequencing_data/out/3/corrected/configs/config.info']" finished abnormally, OS return value: -6 None I wonder why is it happening and how to solve it. Thanks!

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes version: 3.15.4

Operating System

OS: Linux-5.4.0-84-generic-x86_64-with-glibc2.27

Python Version

Python version: 3.10.9

Method of SPAdes installation

binaries

No errors reported in spades.log

• [X] Yes

[Maiya19724]

same error

[asl]

@Riverfishstar One of SPAdes intermediate files got corrupted. Usually it's a sign of some I/O problems on the disk storage you're using for scratch files. Likely your system administrator might provide more insights on this.