Align.seqs error in

i am trying to perform alignment for v34 region of my sequences with that of reference for rRNA analysis. but my alignment is showing error. despite repeated attempts at sorting the matter out by changing my reference sequence files with different silva versions, i am getting the same problem. i also set the parameters as guided by mothur team on one of the related posts prior to mine. i am unable to perform this operation. first, i need a link for this genuine template sequence that would align with v34 hypervariable region in my sequences. Also, i need an answer as to how am i going to overcome this challenge facing my alignment. i read patrick schloss suggested using 1.41.2 VERSION but my default version is 1.39.5. need your help in urgency. regards
silva_nr99_v138.1_train_set.fa uncompressed

Hi - we’re actually up to 1.48.0 now and I’d encourage you to use that version. I’m not really sure what you’re struggling with, but I would encourage you to go through the blog post on customizing the region if you aren’t going to be using the V4 region. I would only use something based on the the SILVA reference alignment with align.seqs, not greengenes. But greengenes would be fine, if dated, for use with classify.seqs


Dear Pshloss, i am trying to align my sequences but my align,seqs job is showing waiting to run but it is not working. all other jobs are working perfectly fine. my this job is not showing error. it only reads your job is waiting to run. it is not starting. m stuck on this point. also can you please share the reference template for V34 region compatible with have tried to figure things out but nothing seems to work. please let me know if there is any solution for the first anomaly. i have attached a screenshot of my job waiting to run for hours but not working. regards

Hi - I’m sorry but I really know nothing about galaxy. We don’t support the galaxy version of mothur. I’d encourage you to reach out to the galaxy developers instead.