Bad format "Invalid BED file" Line 1: sequence chrI not found in genome database.
zealot
Charles E Grant
The name given in columns 1 of the BED file has to exactly match the name of a sequence in the FASTA file. Genbank is probably not a great choice for this as they include a lot of meta-data in their sequence names. For example the first sequence in the Genbank FASTA file for Sac. cer. uid 128 is:
>gi|329136676|tpg|BK006934.2| TPA_inf: Saccharomyces cerevisiae S288c chromosome VIII, complete sequence
which clearly doesn’t match any of the sequence names in your BED file.
You could try using the Ensembl Fungi database for Saccharomyces cerevisiae instead. But beware! Those sequences simply named with the number of the chromosome. They aren’t prefixed with ‘chr’. So a typical sequence name would look like:
>I dna:chromosome chromosome:Sc_YJM1248_v1:I:1:198792:1 REF
The sequence name in the BED file has to match the string between the ‘>’ and the first white space, so your BED file would have to have sequence names I, II, III, etc, not chrI, chrII, charIII.
We also have the UCSC version online in the ‘UCSC Other collection’ as sacCer1. They name their sequences chr1, chr2, chr3, etc. That almost matches your BED file, but with Arabic rather than Roman numerals.
Charles
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> I keep getting this error message while using MEME: Bad format "Invalid BED file" Line 1: sequence chrI not found in genome database.
>
> I can't figure out where I did wrong.
> The settings are:
>
> The bed file content:
>
>
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> <Image2.png><Image1.png>
zealot
Aastha Pal
# 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'.
Thanks,
Aastha