Description of bug
When you provide the wrong type for a SPAdes dataset YAML, you will get an error:
== Error == you should specify at least one unpaired, paired-end, or high-quality mate-pairs library!
This happens even when the error isn't the lack of inclusion of unpaired, paired-end, or mate-pairs types but also when you supply a type that doesn't support the reads provided. Specifically I saw this with pacbio where I mistakenly provided css reads given pacbio as type in the YAML file when the type should instead have been single.
spades.log
Fails before even producing a spades.log file
params.txt
spades.py --dataset <dataset_file>.yaml -o ./test
SPAdes version
4.2.0
Operating System
Some Linux HPC
Python Version
Python 3.12
Method of SPAdes installation
Unknown
No errors reported in spades.log
Description of bug
When you provide the wrong
typefor a SPAdes dataset YAML, you will get an error:This happens even when the error isn't the lack of inclusion of
unpaired,paired-end, ormate-pairstypes but also when you supply a type that doesn't support the reads provided. Specifically I saw this withpacbiowhere I mistakenly provided css reads givenpacbioas type in the YAML file when the type should instead have beensingle.spades.log
Fails before even producing a
spades.logfileparams.txt
spades.py --dataset <dataset_file>.yaml -o ./testSPAdes version
4.2.0
Operating System
Some Linux HPC
Python Version
Python 3.12
Method of SPAdes installation
Unknown
No errors reported in spades.log