unique.seqs after filter.seqs Problem

mothur bugs
1

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:
all_H.filter
all_H.trim.contigs.good.unique.good.filter.fasta

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.

2

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

3

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?

4

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.