meme-sea error
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Aastha Pal
Mar 10, 2025, 9:15:30 PMMar 10
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Hi, this is my first time running the motif enrichment analysis. I prepared my input bed and control bed file and I got an error saying my bed is greater than 80MB. To resolve this issue, I subsetted the control file to match the geneid in my input file and saved it as a new bed file. I than ran the SEA analysis and get the following error. I am not sure how to solve this. Any suggestions?
# Warning: Ignoring sequence '>chr9:112224825-112224827(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:112226224-112226226(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:112234299-112234301(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr10:78284641-78284643(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113441825-113441827(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113645463-113645465(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr10:78287196-78287198(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113695378-113695380(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113699659-113699661(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113705910-113705912(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113707633-113707635(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113719007-113719009(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113726813-113726815(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113731515-113731517(+)' because it is too short (2 < 8).
ERROR: No (valid) sequences in multiple FASTA file.
ERROR: There was a problem reading the primary sequence file 'output.bed.fa'.
Thank you,
# Warning: Ignoring sequence '>chr9:112224825-112224827(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:112226224-112226226(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:112234299-112234301(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr10:78284641-78284643(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113441825-113441827(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113645463-113645465(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr10:78287196-78287198(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113695378-113695380(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113699659-113699661(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113705910-113705912(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113707633-113707635(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113719007-113719009(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113726813-113726815(+)' because it is too short (2 < 8).
# Warning: Ignoring sequence '>chr9:113731515-113731517(+)' because it is too short (2 < 8).
ERROR: No (valid) sequences in multiple FASTA file.
ERROR: There was a problem reading the primary sequence file 'output.bed.fa'.
Thank you,
Aastha
cegrant
Mar 10, 2025, 9:26:42 PMMar 10
to MEME Suite Q&A
If you have not already fixed the problem with your BED file, here
are some suggestions. Rather than trimming some control sequences to
a length of 2 as you had done, simply remove enough of them to get make your total (expanded)
sequence length < 80MB. Alternatively, trim each of your control sequences
sufficiently, but remove any sequence that is shorter than 8bp when expanded from the BED file.
Cheers,
T.
are some suggestions. Rather than trimming some control sequences to
a length of 2 as you had done, simply remove enough of them to get make your total (expanded)
sequence length < 80MB. Alternatively, trim each of your control sequences
sufficiently, but remove any sequence that is shorter than 8bp when expanded from the BED file.
Cheers,
T.
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