== 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

[paulamaza]

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 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

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

• Yes

[asl]

Hello

Your SPAdes job was killed. Likely more information could be found in the system log.

[paulamaza]

spades.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?

[asl]

I was talking about system log, not spades.log. You might want to ask your system administrator

[paulamaza]

system.log

Hi Anton, Im attaching the system log, any help is welcome, I don't have any idea .. thanks

[asl]

It seems to be a log from your laptop, not the server you're running SPAdes on

[paulamaza]

ok, thanks. Do you have any idea how I could fix it? maybe is the operating system Monterey? thanks again

[asl]

Your server is running Linux obviously. I would suggest you to ask your system administrator

[RozemarijnVanDerPlaats]

Hi paulamaza, Did you fixed the problem? I have the same error code -9.

[paulamaza]

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 <#965 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AYVJQZQ7NPQUJ3SUU62IB7DVIS6DHANCNFSM5TUDN26A> . You are receiving this because you authored the thread.Message ID: ***@***.***>