# Apollo Create or Update Organism error **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** tool-help, apollo\ **Created:** [May 9, 2025, 11:08am UTC](https://help.galaxyproject.org/t/apollo-create-or-update-organism-error/15397 "2025-05-09T11:08:14Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![trso](https://avatars.discourse-cdn.com/v4/letter/t/9fc29f/32.png) [@trso](https://help.galaxyproject.org/u/trso)\ **Post date:** [May 9, 2025, 11:08am UTC](https://help.galaxyproject.org/t/apollo-create-or-update-organism-error/15397/1 "2025-05-09T11:08:14Z")
hey i had problem with tool “create or update organisme” that used for apollo i tried to change the name of the organism also i found that the name sould be like the fasta name but the same error and when the tool faild i need to change to another name or the tool shows another issue. any solution thank u. "`INFO:root:curl [https://usegalaxy.eu/apollo\_api/user/loadUsers](https://usegalaxy.eu/apollo_api/user/loadUsers) -H ‘Content-Type: application/json’ -d ‘{“userId”: “a.oua@edu.umi.ac.ma”, “username”: “XXXXXXXXX”, “password”: “XXXXXXXXX”}’ INFO: **main** :Determining if add or update required INFO:root:curl [https://usegalaxy.eu/apollo\_api/organism/findAllOrganisms](https://usegalaxy.eu/apollo_api/organism/findAllOrganisms) -H ‘Content-Type: application/json’ -d ‘{“organism”: “artegeSNAP101 (gx121028)”, “username”: “XXXXXXXXX”, “password”: “XXXXXXXXX”}’ INFO: **main** : Adding Organism INFO:root:curl [https://usegalaxy.eu/apollo\_api/organism/addOrganism](https://usegalaxy.eu/apollo_api/organism/addOrganism) -H ‘Content-Type: application/json’ -d ‘{“commonName”: “artegeSNAP101 (gx121028)”, “directory”: “/data/dnb01/apollo/196815973”, “publicMode”: false, “genus”: “Artemisia”, “species”: “ifranensis”, “username”: “XXXXXXXXX”, “password”: “XXXXXXXXX”}’ Traceback (most recent call last): File “/opt/galaxy/shed\_tools/toolshed.g2.bx.psu.edu/repos/gga/apollo\_create\_or\_update/9e7b8c7185ad/apollo\_create\_or\_update/create\_or\_update\_organism.py”, line 215, in data = wa.organisms.add\_organism( File “/usr/local/tools/\_conda/envs/mulled-v1-6e30e94176c826cd507c7589aec34fbb1f15b9501101942752ee5cacfab9ba49/lib/python3.9/site-packages/decorator.py”, line 232, in fun return caller(func, \*(extras + args), \*\*kw) File “/usr/local/tools/\_conda/envs/mulled-v1-6e30e94176c826cd507c7589aec34fbb1f15b9501101942752ee5cacfab9ba49/lib/python3.9/site-packages/apollo/decorators.py”, line 8, in raise\_error\_decorator r = fn(\*args, \*\*kwargs) File “/usr/local/tools/\_conda/envs/mulled-v1-6e30e94176c826cd507c7589aec34fbb1f15b9501101942752ee5cacfab9ba49/lib/python3.9/site-packages/apollo/organisms/ **init**.py”, line 66, in add\_organism response = self.post(‘addOrganism’, data) File “/usr/local/tools/\_conda/envs/mulled-v1-6e30e94176c826cd507c7589aec34fbb1f15b9501101942752ee5cacfab9ba49/lib/python3.9/site-packages/apollo/client.py”, line 82, in post raise Exception(“Unexpected response from apollo %s: %s” % Exception: Unexpected response from apollo 504: 504 Gateway Time-out # 504 Gateway Time-out * * * nginx/1.20.1 `" ---
**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:** [May 9, 2025, 5:25pm UTC](https://help.galaxyproject.org/t/apollo-create-or-update-organism-error/15397/2 "2025-05-09T17:25:01Z")
Welcome @trso The timeout message can be temporary. Have you tried again? If you still need help, would you please either set your history to a shared state then post the link back here, or you can screenshot everything on the Job Details view (with any input datasets expanded to show the peek view). We can help to double check the parameters. Part of your message is explaining a type of mismatched data entry. How to do this is in this topic: > [@How to get faster help with your question](https://help.galaxyproject.org/t/how-to-get-faster-help-with-your-question/11469/1): > > ## **How to get faster help with your question** > > We love details! 🧑‍🔬 Consider [**Sharing your History**](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) or posting screenshots of your [**Job Information Details**](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) page. > > Please confirm the [**Server URL**](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting_reporting.html) (your web browser at the top!) and any [**Tutorial**](https://training.galaxyproject.org/) links involved. Thanks and let’s start there! 🙂 XREF → [Hands-on: Refining Genome Annotations with Apollo (prokaryotes) / Refining Genome Annotations with Apollo (prokaryotes) / Genome Annotation](https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/tutorial.html) ---
**Author:** ![trso](https://avatars.discourse-cdn.com/v4/letter/t/9fc29f/32.png) [@trso](https://help.galaxyproject.org/u/trso)\ **Post date:** [May 10, 2025, 6:04am UTC](https://help.galaxyproject.org/t/apollo-create-or-update-organism-error/15397/3 "2025-05-10T06:04:34Z")
Thank u @jennaj for replaying yes i already tried today again, but i got the same error this is the link of my shared history > **[Galaxy](https://usegalaxy.eu/published/history?id=91b982cdf65adef4)** > > Galaxy is a community-driven web-based analysis platform for life science research. ---
**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:** [May 12, 2025, 7:04pm UTC](https://help.galaxyproject.org/t/apollo-create-or-update-organism-error/15397/4 "2025-05-12T19:04:30Z")
Hi @trso Thanks for sharing the history! The problem is on the EU server from what I can tell. I also had a test case fail. Let’s ask one of the EU administrators for help. Hi @wm75 – the tool is reporting timeout issues. All ok? Another example job → [Galaxy](https://usegalaxy.eu/datasets/4838ba20a6d86765b03e92b34176d52f/details) based [on this tutorial](https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/tutorial.html). ---
**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:** [July 8, 2025, 11:59pm UTC](https://help.galaxyproject.org/t/apollo-create-or-update-organism-error/15397/6 "2025-07-08T23:59:20Z")
This error is still presenting, and is an issue on the server. Let’s ask the EU admins again for help, Hi @wm75 – I can still reproduce this, any status updates you can share? There are two common error classes, and other situations possible! 1. Busy server, or some server issue 2. Usage error: naming conflict 3. Pending clarification: organism naming “rules” 4. Not registered at all! Let’s revisit from here, and hopefully we can get it resolved! 🙂 ---
**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 18, 2026, 12:05am UTC](https://help.galaxyproject.org/t/apollo-create-or-update-organism-error/15397/7 "2026-04-18T00:05:37Z")