-
Notifications
You must be signed in to change notification settings - Fork 135
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Error == system call for: config.info #1331
Comments
There are no errors in attached |
It is the correct file. The error is: == Error == system call for: "['/hpc/dla_mm/anasantos/data/miniconda3/envs/unicycler_env/bin/spades-core', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/config.info', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/isolate_mode.info']" finished abnormally, OS return value: 2 |
Looks like you redirected output from several runs into a single output directory – spades.log contains intermixed lines. This is not going to work. |
I only did: unicycler -1 namefile_1.fastq.gz -2 namefile_2.fastq.gz -l namefile.fastq -o name_of_directory |
Description of bug
I was running Unicycler to assemble a hybrid genome and encountered the following error related to SPAdes:
WARNING: Try to use logger before create one. Level=ERROR. Message=File /hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/config.info doesn't exist or can't be read!
== Error == system call for: "['/hpc/dla_mm/anasantos/data/miniconda3/envs/unicycler_env/bin/spades-core', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/config.info', '/hpc/dla_mm/anasantos/data/202301_Efaecalis/data/hybrid_genomes/M508826_hybrid/spades_assembly/K111/configs/isolate_mode.info']" finished abnormally, OS return value: 2
I do not know what this is about. I usually do this all the time and never got this error before.
Could You help to identify the problem?
Thank you in advance
spades.log
spades.log
params.txt
params.txt
SPAdes version
3.15.4
Operating System
I am using a server (HPC)
Python Version
No response
Method of SPAdes installation
conda
No errors reported in spades.log
The text was updated successfully, but these errors were encountered: