# Prokka - gbk file misalign in txt file -- Data is in NCBI's gbk format

**URL:** <https://help.galaxyproject.org/t/prokka-gbk-file-misalign-in-txt-file-data-is-in-ncbis-gbk-format/1597>\
**Category:** usegalaxy.org support\
**Tags:** assembly, datatype\
**Created:** [June 24, 2019, 1:50am UTC](https://help.galaxyproject.org/t/prokka-gbk-file-misalign-in-txt-file-data-is-in-ncbis-gbk-format/1597 "2019-06-24T01:50:08Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![czs](https://avatars.discourse-cdn.com/v4/letter/c/f19dbf/32.png) [@czs](https://help.galaxyproject.org/u/czs)\
**Post date:** [June 24, 2019, 1:50am UTC](https://help.galaxyproject.org/t/prokka-gbk-file-misalign-in-txt-file-data-is-in-ncbis-gbk-format/1597/1 "2019-06-24T01:50:08Z")

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Hi all,

I was using Prokka on public server Galaxy Main [[https://usegalaxy.org](https://usegalaxy.org)] to do assembly for my bacterial genome. Everything went smooth. However it appears that wording/spacing in gbk output file downloaded as txt format are all misplaced/aligned.

Is that any way to solve this or can we download gbk file in different format (rather than txt only)? Thanks

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [June 24, 2019, 4:54pm UTC](https://help.galaxyproject.org/t/prokka-gbk-file-misalign-in-txt-file-data-is-in-ncbis-gbk-format/1597/2 "2019-06-24T16:54:34Z")

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Download the data in `.gbk` format and open it this way:

[https://fileinfo.com/extension/gbk](https://fileinfo.com/extension/gbk)

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**Author:** ![czs](https://avatars.discourse-cdn.com/v4/letter/c/f19dbf/32.png) [@czs](https://help.galaxyproject.org/u/czs)\
**Post date:** [June 25, 2019, 4:02am UTC](https://help.galaxyproject.org/t/prokka-gbk-file-misalign-in-txt-file-data-is-in-ncbis-gbk-format/1597/3 "2019-06-25T04:02:24Z")

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Yes Jenna, but is that possible to download as .gbk? I tried but it was .txt. Any way to do it (and again sorry for my stupid question!)?

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [June 25, 2019, 6:03pm UTC](https://help.galaxyproject.org/t/prokka-gbk-file-misalign-in-txt-file-data-is-in-ncbis-gbk-format/1597/4 "2019-06-25T18:03:28Z")

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Hi @czs

No problems, let me try to explain with more detail.

I downloaded a test dataset (output from `Prokka`) and the `gbk` formatting is correct. It is just plain text formatting. Not “tabular”.

The format was designed and specified by NCBI, but all data is patterned in a specific way.

Compare your output to this example and you’ll notice that it matches up: [https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html](https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html)

If you want to use some tool that requires the `.gbk` extension, change the file extension after downloading the data. Tool examples are in my original reply.

The `Prokka` tool creates many outputs in Galaxy and some are parsed into other formats (fasta, tabular, txt). So if you don’t specifically need `.gbk`, review those.

_Note_ Any data that is in `txt` format may have spaces, tabs, or missing values for some columns. These are often custom report styles. It is just how the output was formatted by the original tool authors. Preserving that formatting is important in many downstream use cases.

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<div class="post-metadata">

**Author:** ![czs](https://avatars.discourse-cdn.com/v4/letter/c/f19dbf/32.png) [@czs](https://help.galaxyproject.org/u/czs)\
**Post date:** [June 26, 2019, 1:03am UTC](https://help.galaxyproject.org/t/prokka-gbk-file-misalign-in-txt-file-data-is-in-ncbis-gbk-format/1597/5 "2019-06-26T01:03:40Z")

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Hi @jennaj

I see ! thanks for your help !