ablab
Error == system call for: config.info
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
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
- [X] Yes
Could You help to identify the problem?
There are no errors in attached spades.log file. Will you please attach a correct one from failed run?
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