I am new to galaxy and i am using metagenomic data after unqiue.seqs step i use the unique.reads for alignment using align.seq with greengeen 16 S alignment reference database but it showed error Like this Reading in the alignment.template.dat template sequences... [WARNING]: We found more than 25% of the bases in sequence 4484395 to be ambiguous. Mothur is not setup to process protein sequences.
As the error states, a protein fasta dataset cannot be used as input. Nucleotide fasta is required.
I retested the tool using the sample data in this tutorial (nucleotide) and it worked fine, so I don't think there is a tool problem. http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
If your input is in nucleotide format, and the job still errors this way, please send in a bug report if working at https://usegalaxy.org or can reproduce the problem there. If there is a new bug or suspected bug, we will want to look at it. After review, we will reply with usage advice or get the bug fixed. Please include a link to this question in the comments of the bug report so we can link the two. https://galaxyproject.org/issues/
Galaxy tutorials: https://galaxyproject.org/learn/
Galaxy support FAQs: https://galaxyproject.org/support/
Hope that helps! Jen, Galaxy team