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Old 01-12-2015, 02:02 PM   #1
morning latte
Location: MI

Join Date: Jun 2013
Posts: 91
Default blastall error

Hello experts,

I have had no problem running blastall using the command below so far.

blastall -i query.fa -d database -p blastx -e 1e-5 -a 8 -o output.txt

And all of sudden, I am getting the same warning message as below. I even tried the same query file that was run fine without problem last time but it wasn't run fine this time generating the warning message.

[blastall] WARNING: contig-100_131270: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options.

Could anyone give me any comment on this? Any help would be greatly appreciated.
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Old 01-12-2015, 10:49 PM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

What is the sequence for contig-100_131270, can you see anything odd like invalid nucleotides?
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