ablab
finished abnormally, err code: 2
Description of bug
Errors happend when I use spades in conda environment.
== Error == exception caught: <class 'joblib3.my_exceptions.JoblibSystemExit'>
======= SPAdes pipeline finished abnormally and WITH WARNINGS!
=== Pipeline warnings:
- 57 def warning(warn_str, log=None, prefix=""): ======= Warnings saved to /mnt/hgfs/ubt22share/assemble1/warnings.log
=== ERRORs:
- /home/caiqihang/anaconda3/envs/spades/share/spades-3.13.0-0/share/spades/spades_pipeline/support.py in error(err_str='system call for: "['gzip', '-f', '-7', '/mnt/hgf...0_0.cor.fastq']" finished abnormally, err code: 2', log=None, prefix='')
- exception caught: <class 'joblib3.my_exceptions.JoblibSystemExit'>
Please tell me how to deal with the issue. Thank you!
spades.log
params.txt
SPAdes version
v3.13.0
Operating System
Linux-6.2.0-33-generic-x86_64-with-glibc2.35
Python Version
Python 3.11.4
Method of SPAdes installation
conda
No errors reported in spades.log
- [X] Yes
You are using ancient SPAdes 3.13.0. Does the problem reproduces with the latest SPAdes 3.15.5?
You are using ancient SPAdes 3.13.0. Does the problem reproduces with the latest SPAdes 3.15.5?
I can not install the SPAdes 3.15.5 successfully. New issues happened.
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.35=0
- python=3.9 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.35
I can not install the SPAdes 3.15.5 successfully. New issues happened.
We do not maintain conda packages. You'd better report this to conda.