spades
spades copied to clipboard
== Error == system call for: "['/srv/conda/envs/de_novo_example/share/spades-3.11.1-4/bin/spades', '/home/jovyan/genomics_de_novo_temp/working_dir/spades_default_assembly/K21/configs/config.info']" finished abnormally, err code: -9
Description of bug
Hello Good day. I am Paula Maza and currently working on a microbial metagenomics dataset. I am new to shotgun metagenomics and hoping to learn along the way. I am using SPAdes v. 3.11.1 through binder server. However, I keep getting the error below and I can't seem to find the solution to fix this error. Any ideas are welcome, thanks
spades.log
== Error == system call for: "['/srv/conda/envs/de_novo_example/share/spades-3.11.1-4/bin/spades', '/home/jovyan/genomics_de_novo_temp/working_dir/spades_default_assembly/K21/configs/config.info']" finished abnormally, err code: -9
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. spades.log
params.txt
Command line: /srv/conda/envs/de_novo_example/bin/spades.py -1 /home/jovyan/genomics_de_novo_temp/working_dir/BCep_R1_QCd_err_cor.fastq.gz -2 /home/jovyan/genomics_de_novo_temp/working_dir/BCep_R2_QCd_err_cor.fastq.gz -o /home/jovyan/genomics_de_novo_temp/working_dir/spades_default_assembly -t 4 --only-assembler
System information: SPAdes version: 3.11.1 Python version: 3.6.10 OS: Linux-4.15.0-166-generic-x86_64-with-debian-buster-sid
Output dir: /home/jovyan/genomics_de_novo_temp/working_dir/spades_default_assembly Mode: ONLY assembling (without read error correction) 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/jovyan/genomics_de_novo_temp/working_dir/BCep_R1_QCd_err_cor.fastq.gz'] right reads: ['/home/jovyan/genomics_de_novo_temp/working_dir/BCep_R2_QCd_err_cor.fastq.gz'] interlaced reads: not specified single reads: not specified Assembly parameters: params.txt
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: /home/jovyan/genomics_de_novo_temp/working_dir/spades_default_assembly/tmp Threads: 4 Memory limit (in Gb): 28
SPAdes version
3.11.1
Operating System
macOS Monterey 12.0.1
Python Version
3.6.10
Method of SPAdes installation
conda
No errors reported in spades.log
- [X] Yes
Hello
Your SPAdes job was killed. Likely more information could be found in the system log.
Hi Anton, thanks for the reply. Im attaching the log, Ive tried several times and always get the same issue. how I can fix it?
I was talking about system log, not spades.log. You might want to ask your system administrator
Hi Anton, Im attaching the system log, any help is welcome, I don't have any idea .. thanks
It seems to be a log from your laptop, not the server you're running SPAdes on
ok, thanks. Do you have any idea how I could fix it? maybe is the operating system Monterey? thanks again
Your server is running Linux obviously. I would suggest you to ask your system administrator
Hi paulamaza, Did you fixed the problem? I have the same error code -9.
Hi, sorry for my delay. No
El vie, 6 may 2022 a las 8:48, RozemarijnVanDerPlaats (< @.***>) escribió:
Hi paulamaza, Did you fixed the problem? I have the same error code -9.
— Reply to this email directly, view it on GitHub https://github.com/ablab/spades/issues/965#issuecomment-1119309932, or unsubscribe https://github.com/notifications/unsubscribe-auth/AYVJQZQ7NPQUJ3SUU62IB7DVIS6DHANCNFSM5TUDN26A . You are receiving this because you authored the thread.Message ID: @.***>