== Error == system call for: "['SPAdes-3.15.5-Linux/bin/spades-hammer', 'spades_test/corrected/configs/config.info']" finished abnormally, OS return value: -11

[Liuyw1217]

Description of bug

During the execution of 'spades.py --test', the process terminated abnormally with the following error message:
== Error == system call for: "['SPAdes-3.15.5-Linux/bin/spades-hammer', 'spades_test/corrected/configs/config.info']" finished abnormally, OS return value: -11

spades.log

Command line: /home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades.py --test

System information:
SPAdes version: 3.15.5
Python version: 3.7.12
OS: Linux-5.15.0-97-generic-x86_64-with-debian-bookworm-sid

Output dir: /home4/liuyw/project/project2-virus/test-data/Cheng-data/spades_test
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
Standard mode
For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/home4/liuyw/software/SPAdes-3.15.5-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz']
right reads: ['/home4/liuyw/software/SPAdes-3.15.5-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz']
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: 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: /home4/liuyw/project/project2-virus/test-data/Cheng-data/spades_test/tmp
Threads: 16
Memory limit (in Gb): 250

======= SPAdes pipeline started. Log can be found here: /home4/liuyw/project/project2-virus/test-data/Cheng-data/spades_test/spades.log

/home4/liuyw/software/SPAdes-3.15.5-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz: max reads length: 100
/home4/liuyw/software/SPAdes-3.15.5-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz: max reads length: 100

Reads length: 100

===== Before start started.

===== Read error correction started.

===== Read error correction started.

== Running: /home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer /home4/liuyw/project/project2-virus/test-data/Cheng-data/spades_test/corrected/configs/config.info

0:00:00.000 1M / 11M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.15.5, git revision e757b82
0:00:00.057 1M / 11M INFO General (main.cpp : 76) Loading config from /home4/liuyw/project/project2-virus/test-data/Cheng-data/spades_test/corrected/configs/config.info
0:00:00.087 1M / 11M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16
0:00:00.087 1M / 11M INFO General (memory_limit.cpp : 54) Memory limit set to 250 Gb
0:00:00.087 1M / 11M INFO General (main.cpp : 86) Trying to determine PHRED offset
0:00:00.093 1M / 11M INFO General (main.cpp : 92) Determined value is 33
0:00:00.093 1M / 11M INFO General (hammer_tools.cpp : 38) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.093 1M / 11M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.094 1M / 11M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 16 files using 16 threads. This might take a while.
The program was terminated by segmentation fault
=== Stack Trace ===
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x421e29]
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x423956]
/lib/x86_64-linux-gnu/libc.so.6(+0x42520) [0x7f0a8b02c520]
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer(cfree+0x10) [0x4849a0]
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x494ffe]
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x495c65]
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x460f67]
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x450515]
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x461d47]
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x457100]
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x416300]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f0a8b013d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f0a8b013e40]
/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer() [0x420681]

== Error == system call for: "['/home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades-hammer', '/home4/liuyw/project/project2-virus/test-data/Cheng-data/spades_test/corrected/configs/config.info']" finished abnormally, OS return value: -11

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.

SPAdes log can be found here: /home4/liuyw/project/project2-virus/test-data/Cheng-data/spades_test/spades.log

Thank you for using SPAdes!

params.txt

Command line: /home4/liuyw/software/SPAdes-3.15.5-Linux/bin/spades.py --test

System information:
SPAdes version: 3.15.5
Python version: 3.7.12
OS: Linux-5.15.0-97-generic-x86_64-with-debian-bookworm-sid

Output dir: /home4/liuyw/project/project2-virus/test-data/Cheng-data/spades_test
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
Standard mode
For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'.
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/home4/liuyw/software/SPAdes-3.15.5-Linux/share/spades/test_dataset/ecoli_1K_1.fq.gz']
right reads: ['/home4/liuyw/software/SPAdes-3.15.5-Linux/share/spades/test_dataset/ecoli_1K_2.fq.gz']
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: 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: /home4/liuyw/project/project2-virus/test-data/Cheng-data/spades_test/tmp
Threads: 16
Memory limit (in Gb): 250

SPAdes version

SPAdes v3.15.5

Operating System

Linux

Python Version

Python 3.7.12

Method of SPAdes installation

binaries

No errors reported in spades.log

• Yes

[asl]

This is a known issue with pre-built binaries. Consider compiling from source