jcmcnch
commented
11 months ago Hi @soluna1,
Thanks for your message. Yes, cutadapt is essential for the pipeline to function. I've never tried running the pipeline on Macs before, but in theory it should work but perhaps the M1 architecture is causing issues? Is that the new chip?
Have you tried manually installing just cutadapt? You don't necessarily need to follow the yaml file so long as the cutadapt version is the same as what I specify in the yaml file. BTW, do the other environments install correctly?
Jesse
Hi,
I'm trying to run the pipeline to get back both 16s and 18s from Parada's primers (515/926).
I'm using a Mac M1 and errors come when attempting to install dependencies form cutadapt-env.yaml.
Could not solve for environment specs The following packages are incompatible ├─ _libgcc_mutex 0.1** does not exist (perhaps a typo or a missing channel); ├─ _openmp_mutex 4.5** does not exist (perhaps a typo or a missing channel); ├─ ca-certificates 2021.1.19** does not exist (perhaps a typo or a missing channel); ├─ cutadapt 3.2** does not exist (perhaps a typo or a missing channel); ├─ dnaio 0.5.0** does not exist (perhaps a typo or a missing channel); ├─ isa-l 2.30.0** does not exist (perhaps a typo or a missing channel); ├─ libgcc-ng 9.3.0** does not exist (perhaps a typo or a missing channel); ├─ libgomp 9.3.0** does not exist (perhaps a typo or a missing channel); ├─ libstdcxx-ng 9.3.0** does not exist (perhaps a typo or a missing channel); ├─ pigz 2.5** does not exist (perhaps a typo or a missing channel); ├─ python-isal 0.4.0** does not exist (perhaps a typo or a missing channel); └─ xopen 1.1.0** does not exist (perhaps a typo or a missing channel).It doesn't work either manually for each package, for instance, the _libgcc_mutex is not available by condo-forge, conda or bioconda channels.
So, are they essential for the pipeline? Any alternative to solve this issue. I really need to retrieve 16s and 18s reads for my seqs.
Thanks!!