Not sure if that is a bug regarding the constructing the tree in this version (2021.11)? I worked with that in version qiime2.2021.8 and haven't seen that using the same code. nice -n 19 qiime phylogeny align-to-tree-mafft-fasttree \ > --i-sequences dada2-rep-seqs/dada2-rep-seqs.qza \ > --o-al…

#1. Making multiple-sequence alignment: mkdir fast_tree_out qiime alignment mafft --i-sequences dada2_output/16S-rep-seqs-dada2.qza --p-n-threads 8 --o-alignment fast_tree_out/16S_rep_seqs_mafft.qza #2. Filtering multiple-sequence alignment: qiime alignment mask --i-alignment fast_tree_out/16S_r…

I did run my above code in qiime2-2021.8 and it worked fine. nice -n 19 qiime phylogeny align-to-tree-mafft-fasttree --i-sequences rep-seqs-deblur.qza --o-alignment aligned-rep-seqs-deblur.qza --o-masked-alignment masked-aligned-rep-seqs.qza --o-tree fasttree-unrooted-tree.qza --o-rooted-…

Hi @MarwaTawfik , I do not see an error. This just looks like you are seeing the information that mafft reports while running, because you are running in --verbose mode (this is why QIIME 2 has a verbose mode, so that by default you do not see the logging messages that various tools report while th…

thanks very much @Nicholas_Bokulich

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