meme create HTML output error

[孙海峰]

Hi, this error has puzzled me a few days, could anyone give me some suggestions?THANKS A LOT!

Failed to write HTML output due to errors processing the XML:

minsites has invalid value "1.31687e+06" at /home/pc/meme/libexec/meme-5.0.2/meme_xml_to_html line 453, <$fh> line 218.

Warning: meme_xml_to_html exited abnormally and may have failed to create HTML output.

[cegrant]

The minsites parameter referred to in the error message should only take integer values, most typically somewhere between 2 and the number of sequences in your input database. It that it's getting set to a large floating point number (1.31687e+06). Could you let us know the exact parameters you used for the run, and if possible forward us a copy of the sequence file? That would help us troubleshoot the problem.

[Yijun Tian]

Hi Cegrant,

I've come across the same error when I was trying to run meme on some big fasta file. Below is my command line.

meme All.From.fa -dna -oc All.From/ -p 5 -nostatus -mod oops -nmotifs 2 -minw 4 -maxw 20 -objfun classic -revcomp -markov_order 0 -maxsize 1000000000

Failed to write HTML output due to errors processing the XML:

minsites has invalid value "6.51344e+06" at /home/user/miniconda3/libexec/meme-5.1.1/meme_xml_to_html line 453, <$fh> line 218.

Warning: meme_xml_to_html exited abnormally and may have failed to create HTML output.

--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[9676,1],0]
  Exit code:    1
--------------------------------------------------------------------------

The input file is just a common fasta file with equal length (40bp) sequences.

Thank you

[cegrant]

The error message and the fact that you've set '-maxsize 1000000000' leads me to guess that you are trying to analyze a sequence file that is much larger than MEME can handle. As a rule of thumb it doesn't make sense to run MEME on a file much larger than 40Mb or so. Keep in mind that MEME is using statistical methods to identity short sequences that are over represented in the input data. Typically a motif has to be present in around 1% of the input sequences for MEME to be able to spot it. Trying to run MEME on huge files (larger than 100Mb) will just cause any motif signal to be lost in the noise, since any given short sequence will occur many times simply by chance.

If you are using a high throughput protocol like ChIP-Seq which generates hundreds of thousands or even millions of raw reads, you should first map your reads to the underlying genome, do peak finding, and then use the sequences from the called peaks as the basis for your MEME analysis. Take a look at the protocol described in Motif-based analysis of large nucleotide data sets using MEME-ChIP and see if it's relevant for your experiment.