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MEME cannot handle 318 sequence?

Hi:

I put a fasta file for MEME like this:

meme input.fasta -mod anr -oc MEME_no_control_motif10 -rna -nmotifs 10 -minw 6 -maxw 10  > log4 2> error4
cat error4
Dataset too large (> 100000).  Rerun with larger -maxsize.

The fasta contains about 318 sequences:

wc -l input.fasta 
636 input.fasta

(636=318*2 because the fasta file also contains coordinates)

Is this normal for MEME, the manual said better no more than 500 primary sequences. What should I to make it run?

Thanks,

rna-seq chip-seq rna-seq genome sequencing
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updated by Alex Reynolds Alex Reynolds • written by Kai_Qi Kai_Qi

Have you tried what the program is telling you to do?

Rerun with larger -maxsize.

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written by GenoMax GenoMax

Thanks for reply. I tried it by using maxsize 0. still get the same results， I just tried to use the first 100 line to run the code, it worked well. I guess my sequence plus the number of sequences exceed the limit of meme； then i tried too add a number of -maxsize 200000, it starts running.

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written by Kai_Qi Kai_Qi

1 answer

Get the total, summed length of the 318 sequences in your FASTA file, e.g. via https://www.danielecook.com/generate-fasta-sequence-lengths/

Set your -maxsize parameter to this value.

More explicitly, the output of the aforementioned one-liner can be quickly piped to a second awk statement to sum all the lengths:

$ awk '$0 ~ ">" {if (NR > 1) {print c;} c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' input.fasta | awk '{ s += $2 } END { print s }'

Using -maxsize 0 works, but it will make meme run more slowly. Speed becomes a real issue, depending on values of minw and maxw. Setting -maxsize correctly will allocate only as much memory as needed.

Via documentation: http://meme-suite.org/doc/meme.html

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written by Alex Reynolds Alex Reynolds

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