# Extract Genomic DNA- Chromosome was not found for hg19

**URL:** <https://help.galaxyproject.org/t/extract-genomic-dna-chromosome-was-not-found-for-hg19/4792>\
**Category:** usegalaxy.org support\
**Tags:** bed\
**Created:** [November 6, 2020, 9:06am UTC](https://help.galaxyproject.org/t/extract-genomic-dna-chromosome-was-not-found-for-hg19/4792 "2020-11-06T09:06:39Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Shira-Fisher](https://avatars.discourse-cdn.com/v4/letter/s/59ef9b/32.png) [@Shira-Fisher](https://help.galaxyproject.org/u/Shira-Fisher)\
**Post date:** [November 6, 2020, 9:06am UTC](https://help.galaxyproject.org/t/extract-genomic-dna-chromosome-was-not-found-for-hg19/4792/1 "2020-11-06T09:06:39Z")

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Hay,  
I am trying to extract the DNA sequence from a bed file that contains “Chromosome”, “Start”, “End” and “Score” but I am getting 0 bytes and a warning message that (17033 warnings, 1st is: Chromosome by name ‘chr1’ was not found for build ‘hg19’.  
Skipped 17033 invalid lines, 1st is #1, “chr1 936092 936483 . 221 .”)

I am using [https://usegalaxy.org/](https://usegalaxy.org/).  
I want the sequence for motif discovery.  
Please help.  
Thank you!

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**Author:** ![patryk.janus](https://avatars.discourse-cdn.com/v4/letter/p/f14d63/32.png) [@patryk.janus](https://help.galaxyproject.org/u/patryk.janus)\
**Post date:** [November 13, 2020, 11:04am UTC](https://help.galaxyproject.org/t/extract-genomic-dna-chromosome-was-not-found-for-hg19/4792/2 "2020-11-13T11:04:51Z")

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Hi,  
I have the same problem. Interestingly, a month ago everything worked fine. I checked it on purpose.  
I used the same bed file, which a I have in Galaxy history. The same file, the same settings, but different results: one success and one failure. In the “View details” bookmark of both analyses I see the same tool version and all the same settings.

I am also using [https://usegalaxy.org/](https://usegalaxy.org/), and I need the sequence for motif discovery.

Where is the problem? Anyone?

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**Author:** ![Ji\_Eun\_Kim](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/ji_eun_kim/32/1956_2.png) [@Ji\_Eun\_Kim](https://help.galaxyproject.org/u/Ji_Eun_Kim)\
**Post date:** [November 20, 2020, 8:43pm UTC](https://help.galaxyproject.org/t/extract-genomic-dna-chromosome-was-not-found-for-hg19/4792/3 "2020-11-20T20:43:14Z")

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Hello,

I am also having the same problem.  
I created a list of my peaks chr, start, end, name of the peak on excel, saved the file as Tab-delimited text, uploaded as interval format on galaxy, and selected hg19 as a reference genome.  
I get the same error message as shown below in the picture.  
Is this a problem on my end? Please help!  
Thank you!!

 ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/c/c45e3f614b4db631cff91606f6a164b481958346.png) ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/1/1bc5034c4fe1e8e534404bf6ff5a9914393e0e28.png) ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/0/05ab811fda4d1a40f6c70d91107b3303109598b6.png)