Hi Ricardo,

This tool requires external data that you'll need to configure. Here's how:

(1) download the 2bit file from UCSC for your genomes into a local directory from here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/

(2) add an entry like this to alignseq.loc (note that you'll need to use tabs to separate the columns: 

--
seq hg19 /galaxy/data/hg19/seq/hg19.2bit
--

(3) try running the tool again.

Best,
J.


On Feb 8, 2013, at 2:28 PM, Perez, Ricardo wrote:

Hello,

I am getting this error when using Extract Genomic DNA (version 2.2.2)

empty
format: fasta, database: hg19
924 warnings, 1st is: Chromosome by name 'chr22' was not found for build 'hg19'. Skipped 924 invalid lines, 1st is #1, "chr22 16256331 16287937 NM_001136213 0 - 16258185 16287885 0 11 346,119,167,45,71,71,138,107,174,115,684, 0,1853,10597,11805,13541,188

We set up a local instance of Galaxy and a local mirror of the UCSC Table browser in our servers.

Thank you for your help,
--Ricardo Perez
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