Error with screen.seqs after alignment

Commands in mothur
1

Hello,

I ran the screen.seqs command following align.segs on mothur v1.35.9:

mothur “#screen.seqs(fasta=BA_undil_132.trim.contigs.good.unique.align, count=BA_undil_132.trim.contigs.good.count_table, summary=BA_undil_132.trim.contigs.good.unique.summary, start=1, end=9583, maxhomop=8, processors=24)”


and received the following in my logfile:

Your count file does not include the sequence end please correct.
Your count file does not include the sequence end|<length please correct.
Your count file does not include the sequence end|homop please correct.
Your count file does not include the sequence homop please correct.
Your count file does not include the sequence start please correct.
Your count file does not include the sequence start|<length please correct.
Your count file does not include the sequence start|end please correct.
Your count file does not include the sequence start|end|<length please correct.
Your count file does not include the sequence start|end|homop please correct.
Your count file does not include the sequence start|homop please correct.

Not sure what this means.

Thank you!

2

This is looking like an issue stemming from not having enough memory … I’ll confirm as soon as I test it.

3

Can you try it with 4-8 processors rather than 24?

4

I did try it with a different number of processors (1-8), and was still getting errors. It turns out I maxed out my allotted memory on our supercomputing system, so I remedied that and so far so good!