I run the workflow as described in QIIME 2 tutorial to perform analysis of microbiome data generated by NGS technology. After achieving taxonomy classification step with success i’m trying to build phylogenetic tree. To perform sequence alignement i run this command
qiime alignment mafft
Noting that i used rep-seqs.qza file generated after clustering by VSEARCH method because to perform this task featuredata [sequence] file is required instead of featuredata [taxonomy].
After running the aforementioned command i received this message :
Plugin error from alignment:
Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’, ‘–parttree’, ‘/tmp/qiime2-archive-mdoea5qz/65ebb549-31b5-4f24-8ef3-958428774fc9/data/dna-sequences.fasta’]’ returned non-zero exit status 1.
I need your help to resolve this problem.