glam2mask FATAL: glam2mask: no motif found in motif_for_mask

[Massa Kassa]

Hi,
I have an issue using glam2mask feature.
I'm trying to mask certain motif to find weaker ones using glam2mask as described in man pages.
I've tried to supply motif in letter-probability matrix (as obtained from standalone glam2 or copied from web result), or in regular expression, but glam2mask returns this error
FATAL: glam2mask: no motif found in motif_for_mask,
(motif_for_mask is a file where I have the motif)

What am I doing wrong? Or is this an recognised bug?

Thanks a lot.

By the way, I need this to discover a motif in GC rich bacteria (73%) and the MEME-suite returns biased result to GC rich motifs which is understandable, becouse they align OK.

Mark



Letter-prob example

letter-probability matrix: alength= 4  w= 41 nsites= 198 E= 1
0.0  0.631313131313  0.358585858586  0.010101010101 
0.156565656566  0.363636363636  0.469696969697  0.010101010101 
0.19696969697  0.257575757576  0.318181818182  0.227272727273 
0.010101010101  0.570707070707  0.419191919192  0.0 
0.227272727273  0.166666666667  0.494949494949  0.111111111111 
0.171717171717  0.414141414141  0.19696969697  0.217171717172 
0.0  0.70202020202  0.272727272727  0.0252525252525 
0.0252525252525  0.267676767677  0.707070707071  0.0 
0.292929292929  0.20202020202  0.247474747475  0.257575757576 
0.00505050505051  0.565656565657  0.393939393939  0.0353535353535 
0.166666666667  0.449494949495  0.29797979798  0.0858585858586 
0.217171717172  0.439393939394  0.0  0.287878787879 
0.0  0.459595959596  0.535353535354  0.00505050505051 
0.10101010101  0.363636363636  0.474747474747  0.0606060606061 
0.222222222222  0.212121212121  0.29797979798  0.267676767677 
0.0  0.585858585859  0.388888888889  0.0252525252525 
0.252525252525  0.0707070707071  0.575757575758  0.10101010101 
0.040404040404  0.388888888889  0.237373737374  0.333333333333 
0.010101010101  0.888888888889  0.030303030303  0.0555555555556 
0.10101010101  0.020202020202  0.878787878788  0.0 
0.444444444444  0.242424242424  0.151515151515  0.161616161616 
0.0252525252525  0.414141414141  0.525252525253  0.0353535353535 
0.141414141414  0.328282828283  0.510101010101  0.020202020202 
0.272727272727  0.20202020202  0.282828282828  0.242424242424 
0.0505050505051  0.494949494949  0.444444444444  0.010101010101 
0.171717171717  0.292929292929  0.444444444444  0.0454545454545 
0.181818181818  0.459595959596  0.146464646465  0.212121212121 
0.0  0.545454545455  0.429292929293  0.0252525252525 
0.121212121212  0.39898989899  0.479797979798  0.0 
0.212121212121  0.338383838384  0.171717171717  0.277777777778 
0.0  0.520202020202  0.449494949495  0.030303030303 
0.0505050505051  0.262626262626  0.666666666667  0.020202020202 
0.126262626263  0.328282828283  0.39898989899  0.146464646465 
0.0505050505051  0.550505050505  0.368686868687  0.030303030303 
0.131313131313  0.323232323232  0.474747474747  0.0707070707071 
0.227272727273  0.252525252525  0.338383838384  0.181818181818 
0.0  0.60101010101  0.368686868687  0.030303030303 
0.0656565656566  0.29797979798  0.590909090909  0.0454545454545 
0.116161616162  0.323232323232  0.368686868687  0.191919191919 
0.0151515151515  0.60101010101  0.338383838384  0.0454545454545 
0.151515151515  0.267676767677  0.580808080808  0.0 

Reg-exp example

[cg][cg][ctg][cg][ag][ct][cg][cg][actg][cg][cg][act]?[cg][cg][actg][cg][ag][ctg]c?g[ac][cg][cg][actg][cg][cg]?[ct][cg][cg][act][cg][cg][cg][cg][cg][acg][cg][cg][cg][cg][cg]
 

[CharlesEGrant]

Hi Mark,

 

I have an issue using glam2mask feature.
I'm trying to mask certain motif to find weaker ones using glam2mask
as described in man pages.
I've tried to supply motif in letter-probability matrix (as obtained
from standalone glam2 or copied from web result), or in regular
expression, but glam2mask returns this error
FATAL: glam2mask: no motif found in motif_for_mask,
(motif_for_mask is a file where I have the motif)

GLAM2 and MEME use different file formats to represent motifs. glam2mask and glam2scan can only use the format produced by GLAM2. The sample motif you provided in your email looks like part of a MEME style motif file, so it wouldn’t work with glam2scan. If you have a GLAM2 output file that doesn’t seem to be working, please forward us copies of the sequence data input and the GLAM2 output file so we can troubleshoot the problem.

By the way, I need this to discover a motif in GC rich bacteria (73%)
and the MEME-suite returns biased result to GC rich motifs which is
understandable, becouse they align OK.

Have you tried running MEME using a custom background generated from the bacterial genome? You might also be able to use discriminative mode in MEME to get better results.

[Massa Kassa]

Hi,

thanks for the quick reply.

I now manage to get it working, problem was, that I've tried to load MEME style motifs (also outputted from glam2) in glam2mask. I didn’t realize, that glam2 style motif is in the .txt file with local alignment of motifs.

Thanks for the tip with the discriminative mode, that helped get rid of most biased motifs.

Thanks a lot.

Mark