# mirdeep2 errors -- Solution: verify input format

**URL:** <https://help.galaxyproject.org/t/mirdeep2-errors-solution-verify-input-format/9779>\
**Category:** usegalaxy.org support\
**Tags:** custom-genome, troubleshooting, reference-genome\
**Created:** [April 2, 2023, 1:32am UTC](https://help.galaxyproject.org/t/mirdeep2-errors-solution-verify-input-format/9779 "2023-04-02T01:32:32Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![pmmugand](https://avatars.discourse-cdn.com/v4/letter/p/bcef8e/32.png) [@pmmugand](https://help.galaxyproject.org/u/pmmugand)\
**Post date:** [April 2, 2023, 1:32am UTC](https://help.galaxyproject.org/t/mirdeep2-errors-solution-verify-input-format/9779/1 "2023-04-02T01:32:33Z")

</div>

Please help me in getting the mirdeep2 novel miRNA identification module working for me. It fails everytime I run it even under different conditions. Here are my settings;

Started tool **MiRDeep2** and successfully added 1 job to the queue.

The tool uses 5 inputs:

- **65: Collapsed reads of MiRDeep2 Mapper on data 19** this is the fasta collapsed file, unmapped
- **33: EBV1\_GCF\_002402265.1\_ASM240226v1.fasta** my genome
- **35: AA1\_856\_Mapping output of MiRDeep2 Mapper on data 33 and data 19 in ARF format** mapped to my virus genone
- **38: ebv mirna.fasta** miRNA from mirbase
- **44: EBV stemloop.fasta** stem loops

What am I doing wrong ? Please help

It produces 5 outputs:

- **71: Tabular output of MiRDeep2 on data 44, data 38, and others**
- **72: MiRDeep2 on data 44, data 38, and others (html report)**
- **73: Prediction accuracy output of MiRDeep2 on data 44, data 38, and others**
- **74: Bed output of MiRDeep2 on data 44, data 38, and others**
- **75: Text output of MiRDeep2 on data 44, data 38, and others**

You can check the status of queued jobs and view the resulting data by refreshing the History panel. When the job has been run the status will change from ‘running’ to ‘finished’ if completed successfully or ‘error’ if problems were encountered

---

<div class="post-metadata">

**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:** [April 13, 2023, 12:31am UTC](https://help.galaxyproject.org/t/mirdeep2-errors-solution-verify-input-format/9779/2 "2023-04-13T00:31:52Z")

</div>

> [@pmmugand](#):
>
> **EBV1\_GCF\_002402265.1\_ASM240226v1.fasta** my genome

For others reading (@pmmugand already has the answer):

When using a custom genome fasta, most tools expect a simplified format. [Working with very large fasta datasets](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_working_with_fasta.html)

There isn’t an FAQ for all formats for all tools – but the tool help should have some examples and link-outs to author resources. Other places to check:

1. GTN tutorials may cover your datatype and/or analysis tools.
2. The author’s resources are also a good place to look: publications, forums
3. General bioinformatics forums can also be helpful.
4. Try searching this forum with keywords like datatypes or tool names.
5. If a particular data format/content works when using a tool directly command-line, it will probably have the same format requirements when using it in Galaxy.

What to search for when troubleshooting?

1. Logs: [Troubleshooting errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html)
2. datatypes
3. error messages

---

<div class="post-metadata">

**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:** [August 14, 2026, 7:28pm UTC](https://help.galaxyproject.org/t/mirdeep2-errors-solution-verify-input-format/9779/3 "2026-08-14T19:28:23Z")

</div>

Closed on August 14, 2026, 7:28pm UTC