Followed the SOP for 16S pyrosequencing up to the point for alignment and came into problem.
My command line was
align.seqs(fasta=sample.shhh.trim.unique.fasta, reference=silva.seed_v119.align (also tried to rename to silva.seed_v119.fasta), flip=t, processors=2)
The program just shut down completely whenever I input this command.
The silva seed file was downloaded from Mothur website, I am using windows10 system with 8GB ram and execute Mothur by double clicking the .exe file.
Please help. Thanks,
Yes, I am using 1.36.1.
It turns out I need to rename the seed file. It is now running fine. Thanks.
I had the same problem running v.1.36.1 on Windows 7.
The program shuts down, with this message in the log file:
mothur > align.seqs(candidate=F86_Fungi.shhh.unique.fasta, template=silva.seed_v119.align, threshold=0.80)
[ERROR]: has occurred in the MothurOut class function mothurConvert. Please contact Pat Schloss at firstname.lastname@example.org, and be sure to include the mothur.logFile with your inquiry.
As suggested, I renamed silva.seed_v119.align (to "v119_silva.txt"), and then it works. No idea why that matters.