create-priors usage

[VA]

Dear MEME team,

I am trying to use create-priors utility to provide prior scores for FIMO. I am following the create-priors usage - http://meme-suite.org/doc/create-priors.html. So i provided list of sequences. Here i am showing two 

>chr1:3118680-3120225::1:3118680-3120225
TCTGATTGGGAAATAAAGTTGCCAGCAGCCAATAGTTGGGCAGAGAGACAGAGGTGGGACATTTAGTAATCCCAGGTAAGAAATGAAGAAGAAAAGAAAGGGTCTGCATCGAGAGGGCCATAGGACGAGCCTGAGGGAGAGACAGCTGAAATGTACATACATGCAGGGGGGAAAGCAGCCCCATCGGGAGTGCTGCTCAGAAAGAACAAGGGCAGTAAGATAAAAATACAGATTTAGTAAGTGTTGACTCAGGACGGCTGGAGGGGAGTGTGTGCTAGCCATGGAGAAGTTTGGAAGTGCCTGATCATTGACCTAGTTAAGACATACTAAAATATAAATGTTGTATGTGAGTGTCTTTCATTCATGAGTCCAGAGCTCTTGGGCATGTGCAGAGCTGCATGAGCACTTGCCAAGAAAATAGAGCTTACCTTTAAATGTTTACCACTACCTGGGTTACTTAAGGAGCAGATGAATTGGAAAGCCCAACCCTGAATGGATGACAAGTCACATTTGCTATATCCCTGAAGGACTCTGGGATCACCTTGCAGACAGCTTTATTTAAGAATTCTCCCCTCTTCAGCCATTGATTGTTGCTTTTATAGACACGAGGGGAGGACATTGACCCACTTCCTTTTCTCAGTCGAATTTCTTTTATCTGCCACAGGATGCATCACAATTTGTAGAGTCTGTAACAGTAGACTTTTTGGTTTTGAAACGAGTGTGGGAGACTTCTATCCTTTCTAATCATTCTCTATGAAATTTTTCACTGAAGATCTACACTGAAGAAGAGGGAAATATATGGACCTGAAGATTCTGTCATTTTCTATTTCACCTAAAACTTACATGGAAAACTAGCAAGGATTAAAGCATTACAATGGAACTTTATAATATCTGCTGCTTTGCCTGCCTTTTTGCATCCCTCCTGCCATCTCTGTACACTCACCCACTTCCTTCTGTTGTCTAGAAACAGGATTTTGCTCAGAAGTCCTGGTTGGGCTGGAGCTCACAGTGTCCCAGCCTAGCCTTGAACTTTCACTGACTCTGCACTTTCTTTGTCTACAGAGTTGGGACTACAGATGGGATTTATCATGCTCAGCTGAGAATATGTTTTGTTTATGCAAAGAGTAAGCACTGTTCATATAGTCATAGGTACTCTTTATGTCTCTTCTTTGCCTTTTCCTTTTTTTCCCCATTGATAAAATATCTTTTCCCATCTGGAGAGAGCTTAATCTTGGCTTTATATCCTTTAGCAGCAGTAACACTTTTGGAAGCGAAGGGAGGAGAATGAGATGTCCCTGGAGAAATTGTTTTCTTAGCCAGTGGCTGCCAGTTTTAGAGAAAACTATGTTTGTCTCCACAGTGACGGAGCAGGAGTGTGCAAGAAAACCCTCTGAGGGTTTGCTTGGATAACAAACATTATGCATCATGGGTCCCAAGTGCATACTTACTTAATGCCAAAAATTTGAAAAATATTTCCAGACAAGTAAGAAGAGGCAGATAGCTTATAAATTAAAATGAATGAATATTAACTGTGGGTGAAATTCA
>chr1:3120294-3121035::1:3120294-3121035
GTGATATGTATCTGTGTTAATTACTTTCCATTTATGTGAAAGACAGTTTGAAATGTGCTAAAATGTGAAACAAATGCATGCAGATTTCCTTCATTTGGGCCAAAATTTTATGTCCTATTTTCCAAAAATATATTTCTTCCAGGAAGAAGCCAAGCTATGTGGCCAGATATGATAAGAGTCTGAATTGCACGCAGCTATTTATAAAGTACTCTGTGTCTGCCATCTGCTCTCCACATTCATCTCTTCTGTGTCCCTCTTTCCTAAGATGCTAGCTGTGACTCGGGAGTGAATGTCACATCTTCCTCCCTGTTTTTATTCTTGTTTCAGCTTAGATCCCTTTCGAGTATCTGAGATCACTTGAGGATTGTCTAATGAAGTTGCAGGCACCCACTTCCTAAGTTTATATTTGCTCTTTAGGTTTTAATTTTTGTTCTTCCATTGGATCAGCAACATATATCTGAAAATATTTTTCTTGCTTCCACTCTGGCCTGAAGGACAACACTCCTGAAGGCTACCAGAGGCCTCTCCAGGAGCTAGGACACCACCAGGACACCTTTTCCATACAACTTACCAGTGCAGGCTTATTGCCTAGTGCTGGGCTTGTCTCTGTTCCCTACAGCAGTTTATTCAACTAAATCTAAATCTAGTGCTAAGGTATTGAATTTTAGAACAACATGATTTTTGTTGTTGTTGTTATTACAAAAAGCAATTGCCTTATTCTATTTGGATGTGTAAAGTAAG

I am also providing the wig score for the entire chromosome. Here i am showing first 10 lines

chr1 0 3000450 0
chr1 3000450 3000465 0.25238
chr1 3000465 3000615 0.50476
chr1 3000615 3000630 0.25238
chr1 3000630 3000937 0
chr1 3000937 3000996 0.25238
chr1 3000996 3001092 0.50476
chr1 3001092 3001102 0.45495
chr1 3001102 3001123 0.22748

I run create-priors as follow

create-priors input.fa sample.wig --parse-genomic-coord

However, I getting following error

Creating priors with alpha=1.0 and beta=10000
FATAL: The maximum observed score was 0.0. Unable to compute priors

Can someone please explain how the input should be configured for create-priors?

Thank you

VA

[CharlesEGrant]

There are a couple of problems here. First, the usage statement for create-priors is:

create-priors [options] <FASTA file> <wiggle file>

That is, any optional parameters have to come before the required parameters. So your create-priors command line should look like

create-priors --parse-genomic-coord input.fa sample.wig

The other problem is that your wiggle file is not actually in wiggle format. It seems to be closer to BED format. Because your wiggle file doesn't follow the wiggle format, create-priors wasn't able to recognize any position scores in it, thus the complaint that the maximum observed score was 0.0. You may need to write a script to convert you scores into legal wiggle format.