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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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== Error == system call for: "['SPAdes-3.15.5-Linux/bin/spades-hammer', 'spades_test/corrected/configs/config.info']" finished abnormally, OS return value: -11 #1297

Closed Liuyw1217 closed 4 months ago

Liuyw1217 commented 4 months ago

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 e757b8216f9a038fb616e9551a2d4891b2d19ad7 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

asl commented 4 months ago

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

daidiy1109 commented 4 weeks ago

module load python/3.8.6 module load gcc/12.2

the paoblem has been solved