Meme/Ame - bad file error
Hi, running into an issue I never saw on my previous HPC, when running the following command from meme/5.1.1:
ame --verbose 1 --oc cluster3_001_genes_ame --scoring avg --method fisher --evalue-report-threshold .05 --control --shuffle-- gencode.vM18.promoters.filtered.fa JASPAR2018_CORE_vertebrates_redundant_pfms_meme.meme
Bad file name.
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FATAL: Template does not contain data section.
Not sure if its something about the format of the motif file, shown below, but have never seen this error previously. Thanks.
MEME version 4
ALPHABET= ACGT
strands: + -
Background letter frequencies
A 0.25 C 0.25 G 0.25 T 0.25
MOTIF MA0002.1 RUNX1
letter-probability matrix: alength= 4 w= 11 nsites= 26 E= 0
0.384615 0.076923 0.115385 0.423077
0.461538 0.076923 0.038462 0.423077
0.153846 0.269231 0.038462 0.538462
0.038462 0.038462 0.000000 0.923077
0.076923 0.000000 0.884615 0.038462
0.076923 0.307692 0.000000 0.615385
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.038462 0.000000 0.961538
0.307692 0.076923 0.000000 0.615385
0.500000 0.076923 0.153846 0.269231
URL http://jaspar.genereg.net/matrix/MA0002.1
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Are there any answers here that help? Centrimo error: Template does not contain data section
Actually I figured out that its not the motif file but the fasta file itself. Something about its formatting. Looks like this:
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