unique.seqs after filter.seqs Problem

Hi, I am processing a Miseq on my Mac.

After running filter.seqs with aligned sequences, I got the results like below.

mothur > filter.seqs(fasta=all_H.trim.contigs.good.unique.good.align, vertical=T, trump=.)

Length of filtered alignment: 610
Number of columns removed: 12814
Length of the original alignment: 13424
Number of sequences used to construct filter: 3030962

Output File Names:

Afterwards, I did run unique.seqs with filtered fasta file and it seemed go through the process. However, the process freezes at some point and I can’t go further. Mac was fine though.

mothur > unique.seqs(fasta=all_H.trim.contigs.good.unique.good.filter.fasta, count=all_H.trim.contigs.good.good.count_table)

2099000 2094790
2100000 2095786
2101000 2096786
[stopp and freezes at this point]

Anyone could tell me what is wrong on this??

I would appreciate if you could help me.
Thank you.

Could it be a memory problem?? How many total sequences? How much ram?

Thank you for your reply. I have MacBook Pro 13" Late 2011 model with 2x2GB DDR3 RAM 1333 MHz. There are 3036962 sequences at this step. Does it need more memory?

The amount of memory needed depends on the amount of unique sequences. Given the number of sequences you are processing and the RAM available, I suspect its a memory issue.