# falco not working in fastqc quality control **URL:** \ **Category:** usegalaxy.org support\ **Tags:** upload, tool-install, fastqc\ **Created:** [February 17, 2025, 12:36am UTC](https://help.galaxyproject.org/t/falco-not-working-in-fastqc-quality-control/14752 "2025-02-17T00:36:52Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![RotonEvan](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rotonevan/32/6777_2.png) [@RotonEvan](https://help.galaxyproject.org/u/RotonEvan)\ **Post date:** [February 17, 2025, 12:36am UTC](https://help.galaxyproject.org/t/falco-not-working-in-fastqc-quality-control/14752/1 "2025-02-17T00:36:52Z")
Falco tool not working in fastqc quality control. Loading tool toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0 failed: Error: Could not find tool with id ‘toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0’. Request URL: [https://usegalaxy.org/api/tools/toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0/build](https://usegalaxy.org/api/tools/toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0/build) Request Method: GET Status Code: 404 Not Found ---
**Author:** ![dadrasarmin](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/dadrasarmin/32/6508_2.png) [@dadrasarmin](https://help.galaxyproject.org/u/dadrasarmin)\ **Post date:** [February 17, 2025, 9:02am UTC](https://help.galaxyproject.org/t/falco-not-working-in-fastqc-quality-control/14752/2 "2025-02-17T09:02:30Z")
Hi, thank you very much for reporting this. I saw that it is available on the [Australian](https://usegalaxy.org.au/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffalco%2Ffalco%2F1.2.4%2Bgalaxy0&version=latest) and [European](https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffalco%2Ffalco%2F1.2.4%2Bgalaxy0&version=latest) instances but not on the [US instance](https://usegalaxy.org/tools/list?help=falco). If you just need to test the tool, maybe you can use the other instances. I am not sure how to contact the admins from the US and inquire about this. But I am sure they will find this report and answer to it. Best, Armin ---
**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:** [February 19, 2025, 12:42am UTC](https://help.galaxyproject.org/t/falco-not-working-in-fastqc-quality-control/14752/3 "2025-02-19T00:42:53Z")
Thanks for request this @RotonEvan and thanks for confirming @RotonEvan The request is now here and includes the workaround (use FastQC instead). → [Install Falco at ORG · Issue #927 · galaxyproject/usegalaxy-tools · GitHub](https://github.com/galaxyproject/usegalaxy-tools/issues/927) If you are running the tutorial’s workflow, you can replace the tool directly 1-for-1 with FastQC, then reconnect the noodles. Thanks again! 🛠 ---
**Author:** ![RotonEvan](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rotonevan/32/6777_2.png) [@RotonEvan](https://help.galaxyproject.org/u/RotonEvan)\ **Post date:** [February 19, 2025, 6:21pm UTC](https://help.galaxyproject.org/t/falco-not-working-in-fastqc-quality-control/14752/4 "2025-02-19T18:21:41Z")
So I’ve tried Falco on the European instance and FastQC on the US instance as the suggested workaround. I got errors in both cases, can you tell me if I’m doing something wrong somewhere? **Falco on European instance** ![Screenshot 2025-02-18 at 20.21.26](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/9/9eca2f6fe1b586504bfd499dc5b40fed7aae1dd4.png) ![Screenshot 2025-02-18 at 20.21.43](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/38fdefc194baedeeba91c724f7cd9561e14239ed.png) **FastQC on US instance** ![Screenshot 2025-02-19 at 13.18.56](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/a/af1c184a6ad683f19db6eb3d4c80669b68d2d8d8.png) ![Screenshot 2025-02-19 at 13.19.09](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/1/11db47664abd03c7d2bd3e5a5ecee677f5987d97.png) ![Screenshot 2025-02-19 at 13.19.17](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/a/a9828ed9f64051b64f15ce9c45ba00c1fc7feb4a.png) Please let me know if I need to provide any other information regarding the errors. I’m following the **[Reference-based RNA-Seq data analysis](https://usegalaxy.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#reference-based-rna-seq-data-analysis)** tutorial on Transcriptomics. ---
**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:** [February 19, 2025, 6:45pm UTC](https://help.galaxyproject.org/t/falco-not-working-in-fastqc-quality-control/14752/5 "2025-02-19T18:45:39Z")
Hi @RotonEvan This is the error message from the tool. > uk.ac.babraham.FastQC.Sequence. **SequenceFormatException: ID line didn’t start with ‘@’** It means that the input fastqsanger dataset is malformed. This could be from a partial data upload, or the original file _before loading it to Galaxy_ had a problem. This is good and it part of the quality assurance checks! You’ll need to find and upload the full and complete data file to Galaxy. Please let us know if this helps! 🙂 XRef → [Hands-on: NGS data logistics / NGS data logistics / Introduction to Galaxy Analyses](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html) ---
**Author:** ![RotonEvan](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rotonevan/32/6777_2.png) [@RotonEvan](https://help.galaxyproject.org/u/RotonEvan)\ **Post date:** [February 21, 2025, 12:15am UTC](https://help.galaxyproject.org/t/falco-not-working-in-fastqc-quality-control/14752/6 "2025-02-21T00:15:17Z")
Thank you! This helped. It was probably a partial data upload. I hope Falco will be up and running soon! ---
**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:** [February 21, 2025, 6:59pm UTC](https://help.galaxyproject.org/t/falco-not-working-in-fastqc-quality-control/14752/7 "2025-02-21T18:59:24Z")
Great, glad you have this working and I would expect the other tool to be installed over shortly. 🛠