create-priors problem: "FATAL: The order of sequences in the input wiggle file differs from the order of sequences in the intput FASTA file."

[qin wang]

I am facing the problem "FATAL: The order of sequences in the input wiggle file differs from the order of sequences in the input FASTA file." when I try to use create-priors. 

The following are clear error messages:

"""

Creating priors with alpha=1.0 and beta=10000

Sequence size is 1498357 bases.

Scores were observed for 1498357 bases.

Minimum score is 2.77268

Median score is 3.80554

Maximum score is 15.6714

Sum of scores is 6.4026e+06

Sum of un-normalized priors is 415825

FATAL: The order of sequences in the input wiggle file differs from the order of sequences in the intput FASTA file.

"""

And my command is "create-priors --oc ./test_fimo_with_prior_files ./test_fimo_with_prior_files/ESC.5000.signal.sequence.fa ./test_fimo_with_prior_files/ESC.5000.signal.wig"

Also, here is content of several lines in two input files:

1. test_fimo_with_prior_files/ESC.5000.signal.sequence.fa

>chr6

TGGGAGAGGAGGGTGCGAAGCCAGAGGCTGAGGGCGAAGCTCAAGGGCCCAGAGGGCAGAGCCCGGATGTGGAGAAATAGGCTGAGGGCGGGGCTTGGTGCGCGAGAGGCGGAGCCCAGAGGGGAGCAACAGTTATGAGGGCGGAACTTAGAAACGATGAAGGCTGTAGTAATTGGGCTGAGGGCGGGGCTTAGGAGCACAGAAAGTGGAGTCCAGGTGTAGAGCAATTAGATTGAGGGAGGGGCTTGGAGCATGAGAGGCGGAGTCCGAGTGTGGAGCAACAGGACGAGGGCAGAATTTAAGAGCGCAGAAGGCGGAGCCCCTGCGTGGGCCAGCAGTCTGAGACCG

>chr7

CGGTGTCATGGCCGACGCTCCTCGCACTCCCTTGGAGACTCTAAGTCACACTGCCCTGCTCCCTAGAGGAGAGAGGAAAAGTACTGAAAGGAAGCAGCCAAATTCTTTGACATCCAATCAGAAGCAGGCATGAAGCCAAGAGTTGCCCAATCAGATTAGCGGAAATAGCGAAGGAGTCTCCTGGAAGCAGAGTTGCCATGACAACGCGAGTTTCTAGGGTTCTCTGCTTGCGCCTAGCGCTTGGCAACGCATGGCCACCTCCCTGATGAAATGCAGCCAATAAGAGGGACCCATTTTGTGACGTCAGTAGTTGCCAAGCCGGCTTGCAGAAGCACGCGAGCCGCCCCCTC

>chr3

CAGGGGACCAAAACGTCTACAAGGTAAAGCTGCAGCCTGAAGCGATTTTTTGACCCCCGACACTTAATGGGCTGTCGAAGACCCGGATGTGTCTGGGACTGGCCGAGGTACCCATTAACGCGCCCCCGCTAGACCATCCCCCTTCTCCATTTATGATTGGATTTTCTTAACGCCAATCACTACTTCTCCAGCCACCCATTCCTCAAGGGTGGGGTGAAGTCTTGGTATCCCGCTTTCAATTGGTAGGAGCAAGAAGAGGAGGGCGGGTAGCCGGCTAAGTTCCTCCAATGGCCGTCGTGGCGTGTGGTTAAGGCGGAGTCAAGGCGCTTGGCAGCTGCCCAATCAGCGT

>chr7

TCATTCTCCTTCCCATTTTCTGTTTAAGTTCGGGCGTCCCAGCCCCGCCCAAACAGTGATATTCCCGCCCACTGGATTACCTTCGCTCAAAACAAACCGAAGTTTCCCTTTTGTGTCTCAGCTGGAATCCAAAAAGTTCAGGCTTTTCCCATTGGCTAGGCACCCCTTTCTAGTCCCGCCCACATGGCCTTCTACCTGACATTGTAAACTCCGCCTAACCCAGGTACCTTAGCCTTAGCCCCGCCTACTCACTTTCCTCCCTCTGATTTGCTCCGAATCACGCCCCTCCCACTCTTGGGCGAGCTAGGCGCCTTAGCCCCGCCCACAGCCAGCTTT

>chr4

TTGCTGCATAATCCGGACTCCACAGGTAGGAGGGCTGGGCATTCTAGTGAATGTTGTCGGGAACAAAGGAAGGCCTGGCCCAGCGCCCTCACACACCTCTTACACCGAGCATGCCCGGGCGTCCCGGAACCAGCGAGAACTGGACTTCAGACCCGCCAAGCTGAAAGAAATCCTCATTTCCCCGAAAAGGAGCCGCTCCCAGTGGGAACAAAGAAGAAGCGGGGTGGGGTCTAGGTGGGGCTGAGCCAGGAGGAGCTGGAGAAGCACAGGGGGCGGGTCTAGGAGGAGCCGGTCGTGGGCGGGTCCAAAAGGCGG

2. ESC.5000.signal.wig

variableStep chrom=chr6 span=348

3182967 15.6714

variableStep chrom=chr7 span=350

44405671 15.0179

variableStep chrom=chr3 span=349

90292834 14.5617

variableStep chrom=chr7 span=336

27330690 14.4946

variableStep chrom=chr4 span=315

130520079 12.9171

[cegrant]

Hi Qin,

FATAL: The order of sequences in the input wiggle file differs from the order of sequences in the intput FASTA file

create_priors and FIMO make a single pass through the wiggle file and the fasta file.  Furthermore the regions covered by the wiggle file have to be a sub-set of the regions covered by the FASTA file. This means that the entries in each file have to be in order by the sequence and and the region in the sequence. Your sequences and wiggle file jump from chr7 to chr3, and then back to chr7. Further more you haven't provided genomic coordinates in your FASTA file, but you do in your wiggle file. If you don't provide genomic coordinates in the FASTA file the programs in the MEME Suite will assume that they start at position 1.

Your FASTA file would need to look more like:

>chr3:9029283-9000000

CAGGGGACCAAAACGTCTACAAGGTAAAGCTGCAGCCTGAAGCGATTTTTTGACCCCCGACACTTAATGGGCTGTCGAAGACCCGGATGTGTCTGGGACTGGCCGAGGTACCCATTAACGCGCCCCCGCTAGACCATCCCCCTTCTCCATTTATGATTGGATTTTCTTAACGCCAATCACTACTTCTCCAGCCACCCATTCCTCAAGGGTGGGGTGAAGTCTTGGTATCCCGCTTTCAATTGGTAGGAGCAAGAAGAGGAGGGCGGGTAGCCGGCTAAGTTCCTCCAATGGCCGTCGTGGCGTGTGGTTAAGGCGGAGTCAAGGCGCTTGGCAGCTGCCCAATCAGCGT

>chr4:130520079-130550000

TTGCTGCATAATCCGGACTCCACAGGTAGGAGGGCTGGGCATTCTAGTGAATGTTGTCGGGAACAAAGGAAGGCCTGGCCCAGCGCCCTCACACACCTCTTACACCGAGCATGCCCGGGCGTCCCGGAACCAGCGAGAACTGGACTTCAGACCCGCCAAGCTGAAAGAAATCCTCATTTCCCCGAAAAGGAGCCGCTCCCAGTGGGAACAAAGAAGAAGCGGGGTGGGGTCTAGGTGGGGCTGAGCCAGGAGGAGCTGGAGAAGCACAGGGGGCGGGTCTAGGAGGAGCCGGTCGTGGGCGGGTCCAAAAGGCGG

>chr6:3182967-31840000

TGGGAGAGGAGGGTGCGAAGCCAGAGGCTGAGGGCGAAGCTCAAGGGCCCAGAGGGCAGAGCCCGGATGTGGAGAAATAGGCTGAGGGCGGGGCTTGGTGCGCGAGAGGCGGAGCCCAGAGGGGAGCAACAGTTATGAGGGCGGAACTTAGAAACGATGAAGGCTGTAGTAATTGGGCTGAGGGCGGGGCTTAGGAGCACAGAAAGTGGAGTCCAGGTGTAGAGCAATTAGATTGAGGGAGGGGCTTGGAGCATGAGAGGCGGAGTCCGAGTGTGGAGCAACAGGACGAGGGCAGAATTTAAGAGCGCAGAAGGCGGAGCCCCTGCGTGGGCCAGCAGTCTGAGACCG

>chr7: 130520079-130530000 

CGGTGTCATGGCCGACGCTCCTCGCACTCCCTTGGAGACTCTAAGTCACACTGCCCTGCTCCCTAGAGGAGAGAGGAAAAGTACTGAAAGGAAGCAGCCAAATTCTTTGACATCCAATCAGAAGCAGGCATGAAGCCAAGAGTTGCCCAATCAGATTAGCGGAAATAGCGAAGGAGTCTCCTGGAAGCAGAGTTGCCATGACAACGCGAGTTTCTAGGGTTCTCTGCTTGCGCCTAGCGCTTGGCAACGCATGGCCACCTCCCTGATGAAATGCAGCCAATAAGAGGGACCCATTTTGTGACGTCAGTAGTTGCCAAGCCGGCTTGCAGAAGCACGCGAGCCGCCCCCTC

>chr7-27330690-27340000

TCATTCTCCTTCCCATTTTCTGTTTAAGTTCGGGCGTCCCAGCCCCGCCCAAACAGTGATATTCCCGCCCACTGGATTACCTTCGCTCAAAACAAACCGAAGTTTCCCTTTTGTGTCTCAGCTGGAATCCAAAAAGTTCAGGCTTTTCCCATTGGCTAGGCACCCCTTTCTAGTCCCGCCCACATGGCCTTCTACCTGACATTGTAAACTCCGCCTAACCCAGGTACCTTAGCCTTAGCCCCGCCTACTCACTTTCCTCCCTCTGATTTGCTCCGAATCACGCCCCTCCCACTCTTGGGCGAGCTAGGCGCCTTAGCCCCGCCCACAGCCAGCTTT

Though of course you'd have to provide sequence data for the entire region described by the coordinates.

Your wiggle file would have to look like

variableStep chrom=chr3 span=349

90292834 14.5617

variableStep chrom=chr4 span=315

130520079 12.9171

variableStep chrom=chr6 span=348

3182967 15.6714

variableStep chrom=chr7 span=336

27330690 14.4946