# Unable to use featurecounts tool **URL:** \ **Category:** Uncategorized\ **Tags:** mapping\ **Created:** [December 30, 2020, 5:33am UTC](https://help.galaxyproject.org/t/unable-to-use-featurecounts-tool/5099 "2020-12-30T05:33:41Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![abhilash719](https://avatars.discourse-cdn.com/v4/letter/a/ed655f/32.png) [@abhilash719](https://help.galaxyproject.org/u/abhilash719)\ **Post date:** [December 30, 2020, 5:33am UTC](https://help.galaxyproject.org/t/unable-to-use-featurecounts-tool/5099/1 "2020-12-30T05:33:41Z")
I am unable to assign the correct attributes to my gtf file to use with featurecounts tool. The overall alignment rate is 95.61%, so there is no problem with mapping using bowtie2. While trying to use featurecount, I get the following error: **\> ERROR: no features were loaded in format GTF. The annotation format can be specified by the ‘-F’ option, and the required feature type can be specified by the ‘-t’ option.** **\> The porgram has to terminate.** I annotated the genome using RAST, and uploaded the gtf file from my PC. Since I am using a custom genome, I did the custom build and assigned the genome to both gtf and bam inputs. I am sure there is a problem with identifiers in the genome, bam, and file but I don’t know how do I make identifiers the same. Is there a tool that is used for this problem. Can someone please suggest a solution. I am running short on time and would appreciate any help. I can share my galaxy workflow if someone needs to look at it. Thank you ---
**Author:** ![abhilash719](https://avatars.discourse-cdn.com/v4/letter/a/ed655f/32.png) [@abhilash719](https://help.galaxyproject.org/u/abhilash719)\ **Post date:** [December 30, 2020, 7:05am UTC](https://help.galaxyproject.org/t/unable-to-use-featurecounts-tool/5099/2 "2020-12-30T07:05:24Z")
Now, I uploaded the gtf file from NCBI Ref seq and assigned to it the custom build genome. Though featurecount is now running successfully, but the counts for all genes 0. In short, featurecount is giving output as 0 for all the genes listed in the output. Why is that? ---
**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\ **Post date:** [January 9, 2021, 9:40am UTC](https://help.galaxyproject.org/t/unable-to-use-featurecounts-tool/5099/3 "2021-01-09T09:40:28Z")
Hi @abhilash719, could you provide me more information about the annotation file you are using? Regards ---
**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 15, 2026, 6:23pm UTC](https://help.galaxyproject.org/t/unable-to-use-featurecounts-tool/5099/4 "2026-04-15T18:23:50Z")
2026 Update! See → [Problems with the tool featureCounts: Fatal error: Exit code 255 () - #3 by gallardoalba](https://help.galaxyproject.org/t/problems-with-the-tool-featurecounts-fatal-error-exit-code-255/4837/3) ---
**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 15, 2026, 6:23pm UTC](https://help.galaxyproject.org/t/unable-to-use-featurecounts-tool/5099/5 "2026-04-15T18:23:56Z")
Closed on April 15, 2026, 6:23pm UTC