meme_4.11.0 Failed to write HTML output due to errors processing the XML: evalue_threshold has invalid value - not a number

[Максим Загоскин]

Hello, 

I meet with an error when I use -evt option. I've tried different numbers and it is always the same error:

  

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

evalue_threshold has invalid value "   1e-06" - not a number

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

If some one met with that, what is the problem?

Thank you!

Maxim

[CharlesEGrant]

Hi Maxim,

Unfortunately this is due to a bug in the latest release of the MEME Suite. We'll try to release a fixed version in the next week. In the meantime here is how to work around the problem:

In the 'meme.xml' file in the MEME output directory, you'll find a line that looks like

<evalue_threshold>   1e-06</evalue_threshold>


change that to:

<evalue_threshold>1e-06</evalue_threshold>

(that is, remove the white space in front of the E-value).

Once you've fixed the 'meme.xml' file you can generate the MEME HTML output by running

meme_xml_to_html meme.xml meme.html

You can fix MEME by applying the attached patch, rebuilding, and reinstalling:

patch -p0 -i fix-meme-xml.patch
make clean
make
make install

Our apologies for the inconvenience.

[Максим Загоскин]

Hello Charles,

Thank you for solution.

The patch works well!

As for

meme_xml_to_html meme.xml meme.html

it result in error:

"Use of uninitialized value $id in string eq at /usr/share/perl5/Meme/MemeSAX.pm line 405, <$fh> line 166.

Missing element ambigs"

the last one is just for information. 

Thank you again!

Maxim