Pintail on PC

Commands in mothur
1

I had a question about pintail - I started running it using the chimera.seqs(fasta=filename, template=silva.bacteria.fasta) algorithm in v1.8. It’s been running for about 24h now on a stand alone PC (Windows XP) to examine a file containing about 330 sequences. Note that this was aligned using the Silva.bacteria.fasta alignment database as the template. The screen says its looking a sequence 824 now - I assume its going through all the sequences in the silva database (could be 1,400,000)??? If so, I’m going to pull the plug on that process rather soon. Otherwise, does anyone have an idea of what is going on?

Thanks for the software - it’s great that you have devoted so much time and energy to doing this.

SteveB

2

This must be the training step where the quantiles are calculated. Yeah, I’d probably kill it! I think this takes overnight for 14000 silva sequences, but you only have to do it once. I would also be careful about what you put into the training set because if you add chimeric sequences, you will have problems down the road.