Re: [galaxy-dev] Extract genomic DNA job error

[Jeremy Goecks]

 So we did the following:
 Downloaded the data
 Added the paths to .loc file
 restarted galaxy
 
 We still are getting the following error:
 
 2: Extract Genomic DNA on data 1
 empty
 format: fasta, database: hg19
 56 warnings, 1st is: Chromosome by name 'chr22' was not found for build 
 'hg19'. Skipped 56 invalid lines, 1st is #1, chr22   23487552
 23487738 NM_004914_cds_0_0_chr22_23487553_f 0   +

My guess is that you .loc file is not set up correctly; you'll need to make 
sure that there are tab characters—not spaces—separating the columns. 

If that's not the case, try finding the command line in the galaxy log and 
running it from the command line (make sure to prepend the command with 
'PYTHONPATH=./lib' to get needed Galaxy libraries) and adding debugging 
statements to see why you twobit file isn't being found. Line 200 of 
extract_genomic_dna.py may be the key failure point.

Finally, please keep all replies on the mailing list for community purposes.

Thanks,
J.
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Re: [galaxy-dev] Extract genomic DNA job error

[Jeremy Goecks]

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 1625633116287937 
 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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