Difficulty customizing my reference alignment using align.seqs

I want to determine the start and end positions of primers that I used to target the D1 region of the 28S rRNA. I downloaded the LSU Parc file from the SILVA data base and generated a silva.full_v128.fasta following the “README for the SILVA v128 reference files” instructions.

I generated a Munguiculata.pcr.fasta file with the region targeted for both of my primers.

When I run the command:

align.seqs(fasta=Munguiculata.pcr.fasta, reference=silva.full_v128.fasta, processors=8)

I get the message

“Unable to open Munguiculata.pcr.fasta. Trying output directory /home/vicente/Desktop/mothurbioerosion/Munguiculata.pcr.fasta
Using 8 processors.
Reading in the silva.full_v128.fasta template sequences… Killed”

At this point, I am not sure whether there is a problem with either file or if the sequence Munguiculata.pcr.fasta is not present in the “silva.full_v128.fasta” file.

Any help would be greatly appreciated.

Thank you,

Within mothur, if you run…

For windows…


For Mac/Linux


Do you see Munguiculata.pcr.fasta or silva.full_v128.fasta? If so, what type of computer are you running this on and how much RAM does it have?


Hi Patt,

Im running my commands on Ubuntu 15.10 but realized I didn’t have enough RAM. I created a SWAP file and now everything seems to work. ummary.seqs(fasta=Munguiculata.pcr.align, processors=12)

Using 12 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 69157 72701 357 0 5 1
2.5%-tile: 0 0 0 0 0 1
25%-tile: 0 0 0 0 0 1
Median: 0 0 0 0 0 1
75%-tile: 0 0 0 0 0 1
97.5%-tile: 0 0 0 0 0 1
Maximum: 69157 72701 357 0 5 1
Mean: 69157 72701 357 0 5

of Seqs: 1

Output File Names:

Thank you!