ablab
OS return value: 1
Description of bug
Dear developer:
I have some difficulty in running metaspades, hoping for your help.
spades.log
The program was terminated by segmentation fault === Stack Trace === /public/software/miniconda3/envs/spades4.2.0/bin/spades-hammer(+0x1d339) [0x55c16629f339] /public/software/miniconda3/envs/spades4.2.0/bin/spades-hammer(+0x1db55) [0x55c16629fb55] /lib64/libc.so.6(+0x36400) [0x7fe2dc192400] /lib64/libc.so.6(+0x156cb0) [0x7fe2dc2b2cb0] /public/software/miniconda3/envs/spades4.2.0/bin/spades-hammer(+0x63cc8) [0x55c1662e5cc8] /public/software/miniconda3/envs/spades4.2.0/bin/spades-hammer(+0x654b0) [0x55c1662e74b0] /public/software/miniconda3/envs/spades4.2.0/bin/../lib/libgomp.so.1(+0x19ec4) [0x7fe2dd036ec4] /lib64/libpthread.so.0(+0x7ea5) [0x7fe2dcc28ea5] /lib64/libc.so.6(clone+0x6d) [0x7fe2dc25ab0d]
== Error == system call for: "['/public/software/miniconda3/envs/spades4.2.0/bin/spades-hammer', '/public/project/YTR202409SCS/MG_only_membrane/4_spades_meta/New/spring-MG/corrected/configs/config.info']" finished abnormally, OS return value: 1
params.txt
Dataset parameters: Metagenomic mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/public/project/YTR202409SCS/MG_only_membrane/3_decontamination/spring-MG-1-clean_1.fastq'] right reads: ['/public/project/YTR202409SCS/MG_only_membrane/3_decontamination/spring-MG-1-clean_2.fastq'] 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: [21, 33, 55, 77, 99] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Assembly graph output will use GFA v1.2 format Other parameters: Dir for temp files: /public/project/YTR202409SCS/MG_only_membrane/4_spades_meta/New/spring-MG/tmp Threads: 98 Memory limit (in Gb): 5000000
SPAdes version
SPAdes version: 4.2.0
Operating System
OS: Linux-3.10.0-1160.62.1.el7.x86_64-x86_64-with-glibc2.17
Python Version
Python version: 3.8.20
Method of SPAdes installation
conda
No errors reported in spades.log
- [x] Yes
This is very large dataset, so many things could go wrong... Does it work smaller / subsampled dataset? You might also want to do some quality trimming and try --only-assembler
Thank you for your reply.
The same commands do work on smaller dataset, but in this large dataset it fails. I will try --only-assembler.
I am still wonderding how are large datasets usually assembled using spades except for using --only-assembler ? In order to make co-assemblies I can't split the datasets into small parts.