rep-seq alignment not working

I use Qiime2 2019.7 in VB. I checked all previous posts and tutorials in case you ask.
I am trying to analyze 116 oral samples that were sent to a sequencing company in 8 separate batches. I have tried to work with them separately and merge later on, but my PC couldn’t handle some of the batches that were too large. So I decided to ask them for the biom table which they could generate at 99%, all batches merged and taxonomy assigned after merging. At least that’s what I understood from them. They generate these files with a Qiagen software.
This is what I did:
I converted the biom table to tsv format and created 3 different text files: 1 for frequencies, 1 for rep seqs, and one for taxonomy. Why? because I could only obtain from biom the frequency table by importing to qiime2, and couldn’t import the taxonomy and rep seqs.
The ID 's provided were somehow too mixed up and kept giving me error when importing the fasta file and the taxonomy table. So I decided to give them arbitrary OTU numbers as it used to be (OTU1, OTU2 and so on). This actually worked fine for importing all 3 tables and taxa bar plot was generated nicely. However, for phylogeny analysis I couldn’t follow the mafft alignment of rep seqs:
qiime alignment mafft --i-sequences rep-seq_OTUID.qza --o-alignment aligned-rep-seqs.qza
Plugin error from alignment:

Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’, ‘/tmp/qiime2-archive-nw96c_91/d4c06fcd-4c42-44d5-a382-9ed074bb2203/data/dna-sequences.fasta’]’ returned non-zero exit status 1.

rep-seq_OTUID.qzv (3.8 MB) rep-seq_OTUID.qza (1.6 MB)

I tried solutions you gave before and nothing is working. Could you please help me out?
Also, please tell me if my thread of analysis makes any sense to you or did I just mess up the whole thing…
Thanks for your help,


Hi @milenapi, please re-run the command with the --verbose flag and share the results here - thanks!

Thanks, it was a matter of memory. I had my colleague run it and it worked/


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