# The intermediate output file still exists

**URL:** <https://help.galaxyproject.org/t/the-intermediate-output-file-still-exists/11940>\
**Category:** usegalaxy.eu support\
**Tags:** workflow\
**Created:** [March 16, 2024, 9:59am UTC](https://help.galaxyproject.org/t/the-intermediate-output-file-still-exists/11940 "2024-03-16T09:59:25Z")\
**Posts on this page:** 1\
**Showing post:** 2

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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:** [March 18, 2024, 6:57pm UTC](https://help.galaxyproject.org/t/the-intermediate-output-file-still-exists/11940/2 "2024-03-18T18:57:34Z")

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> [@chenqiang](#):
>
> However, the output file generated in the trim step of my workflow still exists, and my memory is full

Hi @chenqiang

As a guess, the files are used in later steps since those are the post-QA core fastqsanger data, correct?

Read files are usually the largest files in any analysis and can definitely explode the quota usage.

**Try this if quota space is limited:**

1. Remove the _raw read files_ after QA steps
2. Keep _processed read files_ for downstream steps like mapping or assembly
3. After those steps are completed, you can then remove any non-result files.
4. Dataset files organized into collections with different _shapes_ do not consume extra quota space, since those are just references to the original files.
5. But if you introduce any changes to metadata or the file contents, those will then become new independent files that do consume quota.

In short, if you want a tool to work on a datasets, it needs to be retained until that tool completes. Once a file is not needed for any downstream tools, you can safely remove it.

You’ll have a copy of the raw files at the original pre-Upload-to-Galaxy source, so those are not needed on the server, correct?

Xref prior related Q&A – the [Running Galaxy workflows — Planemo 0.75.20 documentation](https://planemo.readthedocs.io/en/latest/running.html#workflow-execution-against-an-external-galaxy) help is what to review next. Or, maybe review some Published Galaxy workflows? Find the search on the **Workflow** link in the masthead of the web application.

- [There was a problem in creating a paired read collection using API - #11 by mvdbeek](https://help.galaxyproject.org/t/there-was-a-problem-in-creating-a-paired-read-collection-using-api/11655/11)
- [Output file problem - #2 by wm75](https://help.galaxyproject.org/t/output-file-problem/11898/2)

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