# Problem with "featurecounts" after MACS2 call peak for ATAC-seq analysis

**URL:** <https://help.galaxyproject.org/t/problem-with-featurecounts-after-macs2-call-peak-for-atac-seq-analysis/15612>\
**Category:** usegalaxy.org support\
**Tags:** troubleshooting, transcriptomics\
**Created:** [June 2, 2025, 3:11pm UTC](https://help.galaxyproject.org/t/problem-with-featurecounts-after-macs2-call-peak-for-atac-seq-analysis/15612 "2025-06-02T15:11:31Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Vu\_Ngo](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/vu_ngo/32/3100_2.png) [@Vu\_Ngo](https://help.galaxyproject.org/u/Vu_Ngo)\
**Post date:** [June 2, 2025, 3:11pm UTC](https://help.galaxyproject.org/t/problem-with-featurecounts-after-macs2-call-peak-for-atac-seq-analysis/15612/1 "2025-06-02T15:11:31Z")

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Hi All,

I running keep getting error while using featureCounts. Here is the message “failed to find the gene identifier attribute in the 9th column of the provided GTF file”

Please helps

Here is entire message

```
    ========== ______ _____  ___________  _____  
    ===== / ____| | | | _ \|__ \| ____| /\ |__ \ 
      ===== | (___| | | | |_) | |__) | |__ / \ | | | |
        ==== \ ___\| | | | _ <| _ /|__ | / /\ \ | | | |
          ==== ____) | |__| | |_) | | \ \| | ____/____ \| |__| |
    ========== | _____/ \____ /| ____/|_| \_\______ /_/ \_\ _____ /
  v2.1.1

```

//========================== featureCounts setting ===========================\  
|| ||  
|| Input files : 1 BAM file ||  
|| ||  
|| dataset\_7659bf36-8d17-4929-9e8d-9c266f828a16.dat ||  
|| ||  
|| Output file : output ||  
|| Summary : output.summary ||  
|| Paired-end : yes ||  
|| Count read pairs : yes ||  
|| Annotation : dataset\_fc252401-2bc3-415b-b247-fd33aebb57ec … ||  
|| Dir for temp files : ./ ||  
|| ||  
|| Threads : 2 ||  
|| Level : meta-feature level ||  
|| Multimapping reads : not counted ||  
|| Multi-overlapping reads : not counted ||  
|| Min overlapping bases : 1 ||  
|| ||  
\============================================================================//

//================================= Running ==================================\  
|| ||  
|| Load annotation file dataset\_fc252401-2bc3-415b-b247-fd33aebb57ec.dat … ||

ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.  
The specified gene identifier attribute is ‘gene\_id’  
An example of attributes included in your GTF annotation is ‘"gene\_id ““peak\_1"”;”’.

---

<div class="post-metadata">

**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\
**Post date:** [June 2, 2025, 10:43pm UTC](https://help.galaxyproject.org/t/problem-with-featurecounts-after-macs2-call-peak-for-atac-seq-analysis/15612/2 "2025-06-02T22:43:36Z")

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Hi @Vu_Ngo,

The error message points on issue with the annotation file and the job setup. featureCount is usually used for gene expression projects, while your annotation file is for peaks. Check this topic:

> [@hisat2 and featurecounts](https://help.galaxyproject.org/t/hisat2-and-featurecounts/7989/10):
>
> Hi Igor, Thanks for the follow up, I repeated the steps, and this time, I did not use any trimming tools. Please use this link to access the workflow; [url: https://usegalaxy.org/u/seraph2/h/rna-seq](https://usegalaxy.org/u/seraph2/h/rna-seq) Seraph

(ignore my typos, like axon instead of exon)

If this does not help, maybe share the history using the following procedure: click at History Options (three horizontal bars icons) in the top right corner of the History panel; select Share or Publish; in the middle window make the history accessible, copy and paste the link here.

Kind regards,  
Igor