I know there are similar topics out there on this but none seemed to answer my question. I have run this code before and it works. I decided to run my data with DADA2 for denoising and then went on to the next step of creating a phylogenetic tree. I just ran it third time by creating a new directory for this analyses but got this same error again.
First the code I used: qiime phylogeny align-to-tree-mafft-fasttree
Plugin error from phylogeny:
Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/var/folders/qd/kjfz98hs7ssch40klxyrpmd00000gn/T/qiime2-archive-p_xkk9qr/b27ae4da-ba4a-4741-9d5a-0b085082b7eb/data/dna-sequences.fasta']' returned non-zero exit status 1.
Debug info has been saved to /var/folders/qd/kjfz98hs7ssch40klxyrpmd00000gn/T/qiime2-q2cli-err-0nbfajgy.log
I have not done anything different this time around. Please help. Thanks!
Edit: I did use the RESCRIPT process to train my classification for taxonomic analyses. there might be an issue there?