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Old 10-26-2011, 07:34 PM   #3
jlc_1020
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Location: Massachusetts

Join Date: Mar 2010
Posts: 11
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Thanks for the help. I think I've almost got this working now. But I'm still getting this error message when I run the fill-aa script:

FIXME: the sequence names not in '>(chr)?\S+' format [?BCuman_ancestor_2.fa.gz.fai
at //FaSlice.pm line 56
FaSlice::throw('FaSlice=HASH(0x10096cc40)', 'FIXME: the sequence names not in \'>(chr)?\S+\' format [\x{1f}\x{8b}\x{8}\x{4}\x{0}...') called at //FaSlice.pm line 92

I'm not sure what this means. The human ancestral sequences are paired with a .bed index file, but the fill-aa script looks for a .fa.gz.fai, so I made one with samtools by doing:

samtools faidx human_ancestor_2.fa | bgzip -c >human_ancestor_2.fa.gz.fai

Is the problem with the format of my index file?
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