Fernando Puente-Sánchez

Calling `04.rundiamond.pl Plastic_trial_merged 1` should run the script excluding the blast against nr (which you did manually) Then restarting from step 5 should work

> Reading COGs hits from /home/poorna/meta_plastic_trial/Plastic_trial_merged/intermediate/04.Plastic_trial_merged.eggnog.diamond Output in /home/poorna/meta_plastic_trial/Plastic_trial_merged/results/07.Plastic_trial_merged.fun3.cog Reading COGs hits from /home/poorna/meta_plastic_trial/Plastic_trial_merged/intermediate/04.Plastic_trial_merged.eggnog.diamond Just noticed that this actually worked for the COGs but failed for the KEGG annotations (it...

The main SqueezeMeta pipeline is designed to work on Linux only. Some users have actually managed to make it work on MacOS (see #97) but we can not provide support...

You can generate it manually, in excel, or write your own bash/perl/python/etc script to do it programatically.

Closing due to lack of activity, feel free to reopen!

I just committed 514e6fd, which adds a `subsetSamples` function to do exactly what you want. This will be released together with SqueezeMeta v1.6, hopefully by the end of this week....

Is `AD_archaea` a complete project or a subset? Are there any bins in `AD_archaea$bins$abund`?

Potentially yes. Can you run `subsetSamples` in the original project?

Also, just want to check... Is this using SQMtools v1.6.0? Or did you copy the function from 514e6fd but are still using the previous version of SqueezeMeta/SQMtools?

What you are doing _should_ be possible in both directions (subsetTax first, and then subsetSamples, or vice versa) so this is a bug, or at least some corner case that...