spades
spades copied to clipboard
Spades is printing errors to stdout
Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above.
Spades prints errors not caught by argparse to stdout instead of stderr.
For an easy example run spades with an empty reads file:
spades.py -1 exists.R1.fastq.gz -2 fake.R2.fastq.gz -o outdir 2> stderr.txt
This is causing errors to not be logged in my pipeline. I am using spades version 3.15.2.
Describe the solution you'd like
Errors printed to stderr.
Describe alternatives you've considered
No response
Additional context
No response
Thanks for the suggestion. We will check whether this could be fixed easily for the next SPAdes versions