Extract Genomic DNA Issue

usegalaxy.org support
#1

I’m trying use the Extract Genomic DNA tool and keep getting the error: 2347 warnings, 1st is: Chromosome by name ‘chr14’ was not found for build ‘hg19’.
Skipped 2347 invalid lines, 1st is #1, “chr14 100241205 100241705 region_0 0 +” Also see attached screenshot of output.

The input file is a bed file after using bedtools intersect intervals and the reference genome used was hg19. Is there a formatting issue with the bed file? Does it need to be converted to a different file type or format in order for the Extract Genomic DNA tool to work?

Thank you!

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#2

Could you share the exact parameters you used?

You can just click the “Run this job again” button (the little arrow circle button in dataset 198) to make it show them.

#3

Screen Shot 2020-12-14 at 9.11.10 AM
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These are my parameters, everything is at the default setting.

#4

Thank you. I’ve been able to replicate the error myself now. It seems it’s as it appears: for some reason I think it’s not recognizing the chromosome names in the hg19 reference. I’ll try to look into where the problem is.

#5

It seems there’s a configuration issue with hg19 on the server. While we’re working on that, you should be able to use “bedtools GetFastaBed” instead. It should be able to perform the same job.

#6

Thank you! I just tried that and it seems to have worked. It gave me one warning: Warning: the index file is older than the FASTA file. Is this something to be concerned about? I included a screenshot of my parameters if that helps

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#7

Great to hear.

I got that warning too, but I wouldn’t worry about it much.