Problems using matrix2meme (MotifUtils.pm - size_full)

[0neN3x]

Hi there,
I get the following error using MEME 4.11.2_1, help please.


wget http://cisbp.ccbr.utoronto.ca/data/1.02/DataFiles/PWMs/Files/M6496_1.02.txt

matrix2meme < <(tail -n+2 M6496_1.02.txt | cut -f2-) > M6496_1.02.meme

Can't call method "size_full" on an undefined value at /home/user/meme/lib/perl/MotifUtils.pm line 385, <STDIN> line 13.

[CharlesEGrant]

I wasn’t able to reproduce this error on a local system using the commands you specified. I did get some warning messages, but they were all of the form

Use of uninitialized value in subtraction (-) at /Users/cegrant/meme_4.11.2/lib/perl/MotifUtils.pm line 407, <STDIN> line 13.

and 

Use of uninitialized value $score in sprintf at /Users/cegrant/meme_4.11.2/lib/perl/MotifUtils.pm line 462, <STDIN> line 13.

and despite the warning messages the output file, M6496_1.02.meme, was correct.

I’d recommend that you check your output file to see if it’s actually OK.

If it’s not OK, I’d double check your execution and Perl library paths to make sure there isn’t an old version of matrix2meme and the supporting libraries hanging around.

I was able to reproduce the error you report if I ran matrix2meme directly on M6496_1.02.txt, since that file is not in the expected matrix format.