# Latest **URL:** https://help.galaxyproject.org/latest.md?page=1 [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) **Page:** 2 --- ## [UseGalaxy.eu: permanent deletion fails with SSL error and storage quota remains unchanged](https://help.galaxyproject.org/t/usegalaxy-eu-permanent-deletion-fails-with-ssl-error-and-storage-quota-remains-unchanged/18481)
**Author:** [@zhuo7752](https://help.galaxyproject.org/u/zhuo7752)\ **Replies:** 1\ **Last updated:** [October 15, 2026, 7:34pm UTC](https://help.galaxyproject.org/t/usegalaxy-eu-permanent-deletion-fails-with-ssl-error-and-storage-quota-remains-unchanged/18481 "2026-10-15T19:34:46Z")
Hello Galaxy Europe team, I am using https://usegalaxy.eu and trying to free storage space after backing up my results. When I select a deleted dataset and choose “Delete (permanently)”, I encounter this error: \[SSL: … --- ## [Prokka\_error\_message\_Argument "1.7.8"](https://help.galaxyproject.org/t/prokka-error-message-argument-1-7-8/8122)
**Author:** [@Dr\_Ahmed\_Hammad](https://help.galaxyproject.org/u/Dr_Ahmed_Hammad)\ **Replies:** 1\ **Last updated:** [June 8, 2022, 3:26pm UTC](https://help.galaxyproject.org/t/prokka-error-message-argument-1-7-8/8122 "2022-06-08T15:26:12Z")
I try to run Prokka but I receive an error message: Argument “Argument “1.7.8” isn’t numeric in numeric lt (\<) at /usr/local/bin/prokka line 259. Picked up \_JAVA\_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/043/189/431… --- ## [Sharing via url](https://help.galaxyproject.org/t/sharing-via-url/18457)
**Author:** [@thobile.bolt](https://help.galaxyproject.org/u/thobile.bolt)\ **Replies:** 1\ **Last updated:** [October 14, 2026, 6:25pm UTC](https://help.galaxyproject.org/t/sharing-via-url/18457 "2026-10-14T18:25:30Z")
Greetings, I am unable to share my history with the user I know is on galaxy, the error says, the user is not a galaxy user, Please help. --- ## [Tiberius indexes missing? How to navigate tool versions to find them!](https://help.galaxyproject.org/t/tiberius-indexes-missing-how-to-navigate-tool-versions-to-find-them/18468)
**Author:** [@thobile.bolt](https://help.galaxyproject.org/u/thobile.bolt)\ **Replies:** 2\ **Last updated:** [October 14, 2026, 6:24pm UTC](https://help.galaxyproject.org/t/tiberius-indexes-missing-how-to-navigate-tool-versions-to-find-them/18468 "2026-10-14T18:24:41Z")
Unable to run Tiberius, model required. --- ## [Help with IQ tree](https://help.galaxyproject.org/t/help-with-iq-tree/18464)
**Author:** [@Katherine\_Gonzalez](https://help.galaxyproject.org/u/Katherine_Gonzalez)\ **Replies:** 3\ **Last updated:** [October 14, 2026, 6:19pm UTC](https://help.galaxyproject.org/t/help-with-iq-tree/18464 "2026-10-14T18:19:31Z")
my Mafft file is unable to create an IQ tree. Any ideas on how to help? --- ## [Cannot access the tutorial material to conduct LefSe anaysis on Galaxy](https://help.galaxyproject.org/t/cannot-access-the-tutorial-material-to-conduct-lefse-anaysis-on-galaxy/18454)
**Author:** [@N123](https://help.galaxyproject.org/u/N123)\ **Replies:** 1\ **Last updated:** [October 14, 2026, 6:15pm UTC](https://help.galaxyproject.org/t/cannot-access-the-tutorial-material-to-conduct-lefse-anaysis-on-galaxy/18454 "2026-10-14T18:15:41Z")
Can anyone provide the tutorial materials for conducting LefSe analysis on Galaxy? The tutorial link shows Repository not found. --- ## [Kraken2 jobs and how these process at UseGalaxy.org](https://help.galaxyproject.org/t/kraken2-jobs-and-how-these-process-at-usegalaxy-org/18474)
**Author:** [@Sangeun\_Lee](https://help.galaxyproject.org/u/Sangeun_Lee)\ **Replies:** 1\ **Last updated:** [October 14, 2026, 5:50pm UTC](https://help.galaxyproject.org/t/kraken2-jobs-and-how-these-process-at-usegalaxy-org/18474 "2026-10-14T17:50:24Z")
Hello, I have several jobs that have remained in the queued state for an unusually long time on usegalaxy.org. Kraken2: Two jobs (SRR24821405 and SRR24821387) have been queued for more than a day, while the other 11 … --- ## [IQ tree not working throwing error](https://help.galaxyproject.org/t/iq-tree-not-working-throwing-error/9896)
**Author:** [@Preet\_Kaur](https://help.galaxyproject.org/u/Preet_Kaur)\ **Replies:** 2\ **Last updated:** [April 18, 2023, 4:29am UTC](https://help.galaxyproject.org/t/iq-tree-not-working-throwing-error/9896 "2023-04-18T04:29:36Z")
Hi Ive ran a couple of trees using the same steps shown in this history successfully however for this specific SRA the tree gave an error output. Could someone help me figure out what went wrong or what the next steps … --- ## [Should metagenomic assembly and MAG-based resistome mobility analysis be performed replicate-wise or using co-assembly?](https://help.galaxyproject.org/t/should-metagenomic-assembly-and-mag-based-resistome-mobility-analysis-be-performed-replicate-wise-or-using-co-assembly/18450)
**Author:** [@MUHAMMAD\_MUKHEED](https://help.galaxyproject.org/u/MUHAMMAD_MUKHEED)\ **Replies:** 1\ **Last updated:** [October 9, 2026, 12:58am UTC](https://help.galaxyproject.org/t/should-metagenomic-assembly-and-mag-based-resistome-mobility-analysis-be-performed-replicate-wise-or-using-co-assembly/18450 "2026-10-09T00:58:23Z")
I am working on a metagenomic study of ARGs in river water samples. I have already performed read-level ARG profiling using ARGs-OAP, and the three biological replicates from each sampling location/time point were analyz… --- ## [Galaxy upload job stuck in ready state and dataset remains 0 B](https://help.galaxyproject.org/t/galaxy-upload-job-stuck-in-ready-state-and-dataset-remains-0-b/18442)
**Author:** [@15802092671](https://help.galaxyproject.org/u/15802092671)\ **Replies:** 1\ **Last updated:** [October 7, 2026, 12:11am UTC](https://help.galaxyproject.org/t/galaxy-upload-job-stuck-in-ready-state-and-dataset-remains-0-b/18442 "2026-10-07T00:11:16Z")
Hi, I am following the Galaxy Training Network Quality Control tutorial and trying to upload the tutorial file: female\_oral2.fastq-4143.gz The file is very small, about 132 KB. I uploaded it from my local computer, b… --- ## [MiRDeep2\_no\_inbuilt\_reference\_genome(whitespace issue with file uploaded)](https://help.galaxyproject.org/t/mirdeep2-no-inbuilt-reference-genome-whitespace-issue-with-file-uploaded/18439)
**Author:** [@nive3437](https://help.galaxyproject.org/u/nive3437)\ **Replies:** 1\ **Last updated:** [October 6, 2026, 11:51pm UTC](https://help.galaxyproject.org/t/mirdeep2-no-inbuilt-reference-genome-whitespace-issue-with-file-uploaded/18439 "2026-10-06T23:51:53Z")
Please provide the built-in reference genome, as we are facing an issue with the uploaded reference genome (white space issue) in miRdeep2 --- ## [NUCmer/MUMmer dotplot job exceeds memory allocation for ~1 Gb alligator gar genomes](https://help.galaxyproject.org/t/nucmer-mummer-dotplot-job-exceeds-memory-allocation-for-1-gb-alligator-gar-genomes/18445)
**Author:** [@micjwol](https://help.galaxyproject.org/u/micjwol)\ **Replies:** 1\ **Last updated:** [October 6, 2026, 11:45pm UTC](https://help.galaxyproject.org/t/nucmer-mummer-dotplot-job-exceeds-memory-allocation-for-1-gb-alligator-gar-genomes/18445 "2026-10-06T23:45:24Z")
I am using Galaxy to compare two whole-genome assemblies of alligator gar (Atractosteus spatula) as part of a male-versus-female genome comparison. The two FASTA assemblies are: - Reference / male: MaleAlligatorGar\_fAt… --- ## [miRge3 reference library not available in the server](https://help.galaxyproject.org/t/mirge3-reference-library-not-available-in-the-server/18424)
**Author:** [@nive3437](https://help.galaxyproject.org/u/nive3437)\ **Replies:** 8\ **Last updated:** [October 5, 2026, 5:43pm UTC](https://help.galaxyproject.org/t/mirge3-reference-library-not-available-in-the-server/18424 "2026-10-05T17:43:37Z")
Admins, please fix the following issue I’m trying to use the miRge3 pipeline for miRNA seq analyses (done using the MGI platform), the miRge3 human library is not available (nor can it be manually uploaded) --- ## [MultiQC Dataset selector stuck](https://help.galaxyproject.org/t/multiqc-dataset-selector-stuck/18437)
**Author:** [@aaak](https://help.galaxyproject.org/u/aaak)\ **Replies:** 3\ **Last updated:** [October 5, 2026, 4:51pm UTC](https://help.galaxyproject.org/t/multiqc-dataset-selector-stuck/18437 "2026-10-05T16:51:53Z")
Hello, I am experiencing an issue with the dataset selector in Galaxy Europe while configuring MultiQC. I have approximately 130 STAR-related datasets in my history. When I open the STAR log output selector in MultiQC,… --- ## [Metatranscriptomic analysis fails to determine pathwasy with HUMAnN](https://help.galaxyproject.org/t/metatranscriptomic-analysis-fails-to-determine-pathwasy-with-humann/18426)
**Author:** [@jenny.gamezroessler](https://help.galaxyproject.org/u/jenny.gamezroessler)\ **Replies:** 3\ **Last updated:** [October 3, 2026, 12:29am UTC](https://help.galaxyproject.org/t/metatranscriptomic-analysis-fails-to-determine-pathwasy-with-humann/18426 "2026-10-03T00:29:48Z")
Hello Galaxy team, i write because i have a problem with the HUMAnN tool (v3.9 + galaxy1) i used on fecal NGS sequences (samples from four days). I have followed the tutorial “Metatranscriptomics analysis using microbio… --- ## [Trimmomatic error in variant analysis tutorial](https://help.galaxyproject.org/t/trimmomatic-error-in-variant-analysis-tutorial/18423)
**Author:** [@Adam\_Haberman](https://help.galaxyproject.org/u/Adam_Haberman)\ **Replies:** 3\ **Last updated:** [October 2, 2026, 11:30pm UTC](https://help.galaxyproject.org/t/trimmomatic-error-in-variant-analysis-tutorial/18423 "2026-10-02T23:30:05Z")
I’m pretty new to Galaxy, so I can’t tell if this error is my fault or not. I am working through the tutorial Identification of somatic and germline variants from tumor and normal sample pairs on usegalaxy. org (The hel… --- ## [Fatal Erreur Exit code 1 sur xcms findChromPeaks (v3.12.0+galaxy4)](https://help.galaxyproject.org/t/fatal-erreur-exit-code-1-sur-xcms-findchrompeaks-v3-12-0-galaxy4/18427)
**Author:** [@Theo](https://help.galaxyproject.org/u/Theo)\ **Replies:** 3\ **Last updated:** [October 1, 2026, 9:58am UTC](https://help.galaxyproject.org/t/fatal-erreur-exit-code-1-sur-xcms-findchrompeaks-v3-12-0-galaxy4/18427 "2026-10-01T09:58:16Z")
Hello, I am writing to report a systematic error when running a job on the Workflow4Metabolomics platform. The xcms findChromPeaks (xcmsSet) tool repeatedly fails during chromatographic peak detection. Job details: … --- ## [Which COI primers are suitable for mylabris pustulata DNA barcoding?](https://help.galaxyproject.org/t/which-coi-primers-are-suitable-for-mylabris-pustulata-dna-barcoding/18421)
**Author:** [@Hina\_Bibi](https://help.galaxyproject.org/u/Hina_Bibi)\ **Replies:** 1\ **Last updated:** [October 1, 2026, 12:13am UTC](https://help.galaxyproject.org/t/which-coi-primers-are-suitable-for-mylabris-pustulata-dna-barcoding/18421 "2026-10-01T00:13:58Z")
I am planning COI DNA barcoding of Mylabris pustulata and would appreciate advice from researchers working with Mylabris or Meloidae. I am considering either the universal COI primers LCO1490/HCO2198 or a universal forw… --- ## [Finding the MultiQC tool](https://help.galaxyproject.org/t/finding-the-multiqc-tool/18429)
**Author:** [@milaisabellebolger](https://help.galaxyproject.org/u/milaisabellebolger)\ **Replies:** 5\ **Last updated:** [September 30, 2026, 11:43pm UTC](https://help.galaxyproject.org/t/finding-the-multiqc-tool/18429 "2026-09-30T23:43:40Z")
Dear Galaxy EU, I am not able to find the MultiQC tool anymore. I used it before, but it does not appear anymore at my tools. Is there any reason I cannot use this anymore? I would like to use the MultiQC to put my many… --- ## [Requested memory issues](https://help.galaxyproject.org/t/requested-memory-issues/18430)
**Author:** [@bsegers](https://help.galaxyproject.org/u/bsegers)\ **Replies:** 1\ **Last updated:** [September 30, 2026, 4:30pm UTC](https://help.galaxyproject.org/t/requested-memory-issues/18430 "2026-09-30T16:30:05Z")
It’s been three weeks now that I haven’t been able to get any results using the GetOrganelle tool : Get organelle from reads (version 1.7.7.1+galaxy0). I keep getting the same error message about the requested memory. "… --- ## [Panaroo 1.8.0+galaxy0 fails on GFF3 collection with FileNotFoundError: input\_directory/\*.gff](https://help.galaxyproject.org/t/panaroo-1-8-0-galaxy0-fails-on-gff3-collection-with-filenotfounderror-input-directory-gff/18269)
**Author:** [@Loc\_Le](https://help.galaxyproject.org/u/Loc_Le)\ **Replies:** 7\ **Last updated:** [September 28, 2026, 5:59pm UTC](https://help.galaxyproject.org/t/panaroo-1-8-0-galaxy0-fails-on-gff3-collection-with-filenotfounderror-input-directory-gff/18269 "2026-09-28T17:59:43Z")
Hello, I encountered what appears to be a wrapper issue in Panaroo (Galaxy wrapper version 1.8.0+galaxy0 on usegalaxy.eu). Input: - Collection of 19 GFF3 files - All files were generated by Bakta - Collection dataty… --- ## [Reference genome for Drosophila issue](https://help.galaxyproject.org/t/reference-genome-for-drosophila-issue/18410)
**Author:** [@Maksym\_Dankovskyy](https://help.galaxyproject.org/u/Maksym_Dankovskyy)\ **Replies:** 7\ **Last updated:** [September 28, 2026, 5:41pm UTC](https://help.galaxyproject.org/t/reference-genome-for-drosophila-issue/18410 "2026-09-28T17:41:03Z")
Hello, I am trying to use RNA-STAR but I don’t believe the proper drosophila genome annotation is available under “built-in reference genome”. The two options are DM3 and release 6 ISO1 MT. However, I am looking specific… --- ## [Unable to save dataset attributes](https://help.galaxyproject.org/t/unable-to-save-dataset-attributes/18416)
**Author:** [@bsegers](https://help.galaxyproject.org/u/bsegers)\ **Replies:** 1\ **Last updated:** [September 24, 2026, 5:08pm UTC](https://help.galaxyproject.org/t/unable-to-save-dataset-attributes/18416 "2026-09-24T17:08:09Z")
I’m trying to change the format of a dataset obtained with AdapterRemoval. When I want to assign a new datatype from fastaqsanger to fasta, I’ve got the message : unable to save dataset attributes. I did this modificatio… --- ## [BEAST2 tool fails with ClassNotFoundException on Galaxy](https://help.galaxyproject.org/t/beast2-tool-fails-with-classnotfoundexception-on-galaxy/18414)
**Author:** [@Sawar](https://help.galaxyproject.org/u/Sawar)\ **Replies:** 1\ **Last updated:** [September 23, 2026, 6:08pm UTC](https://help.galaxyproject.org/t/beast2-tool-fails-with-classnotfoundexception-on-galaxy/18414 "2026-09-23T18:08:55Z")
Continuing the discussion from Installation of BEAST on Galaxy Europe: Dear Galaxy Europe team, I’m trying to run the BEAST2 tool on usegalaxy.eu and the job fails immediately, before the analysis starts. The same XML … --- ## [Galaxy server slow and freezed](https://help.galaxyproject.org/t/galaxy-server-slow-and-freezed/18411)
**Author:** [@karenandreac](https://help.galaxyproject.org/u/karenandreac)\ **Replies:** 1\ **Last updated:** [September 23, 2026, 5:21pm UTC](https://help.galaxyproject.org/t/galaxy-server-slow-and-freezed/18411 "2026-09-23T17:21:15Z")
Hello! Since yesterday I’ve been working with DADA2 in Galaxy.org and it has been very slow, the tool MakeSequenceTable has been freezed without initiating for many hours now. Would you let me know if there are any iss… --- ## [Direct transfer of ~109 GB Novogene RNA-seq data to UseGalaxy.eu and recommended storage](https://help.galaxyproject.org/t/direct-transfer-of-109-gb-novogene-rna-seq-data-to-usegalaxy-eu-and-recommended-storage/18390)
**Author:** [@aaak](https://help.galaxyproject.org/u/aaak)\ **Replies:** 5\ **Last updated:** [September 22, 2026, 12:44pm UTC](https://help.galaxyproject.org/t/direct-transfer-of-109-gb-novogene-rna-seq-data-to-usegalaxy-eu-and-recommended-storage/18390 "2026-09-22T12:44:44Z")
Dear Galaxy community, Following a suggestion from the Galaxy Europe support team, I am posting our question here so that the answer may also be useful to other users. We have a paired-end mRNA-seq dataset consisting o… --- ## [UseGalaxy.fr service updates re: IFB Core Cluster infrastructure shutdown from September 14th to 21st, 2026](https://help.galaxyproject.org/t/usegalaxy-fr-service-updates-re-ifb-core-cluster-infrastructure-shutdown-from-september-14th-to-21st-2026/18409)
**Author:** [@tristan.lefebure](https://help.galaxyproject.org/u/tristan.lefebure)\ **Replies:** 1\ **Last updated:** [September 21, 2026, 7:09pm UTC](https://help.galaxyproject.org/t/usegalaxy-fr-service-updates-re-ifb-core-cluster-infrastructure-shutdown-from-september-14th-to-21st-2026/18409 "2026-09-21T19:09:20Z")
Dear all, Is installing FROGS on usegalaxy\_eu still not possible ? usegalaxy\_fr as an electrical issue, and I can’t find an other alternative… and my training session is next week ;( Thanks --- ## [Installation of FROGS (metagenomics from metabarcoding.usegalaxy.fr) on usegalaxy.eu](https://help.galaxyproject.org/t/installation-of-frogs-metagenomics-from-metabarcoding-usegalaxy-fr-on-usegalaxy-eu/16225)
**Author:** [@andy\_laprie](https://help.galaxyproject.org/u/andy_laprie)\ **Replies:** 2\ **Last updated:** [August 29, 2025, 8:36pm UTC](https://help.galaxyproject.org/t/installation-of-frogs-metagenomics-from-metabarcoding-usegalaxy-fr-on-usegalaxy-eu/16225 "2025-08-29T20:36:54Z")
Hello, Would it be possible to install the metabarcoding tool FROGS on my Galaxy.eu session please? Thank you very much in advance ! AL --- ## [UseGalaxy.org account activation required — no activation email received](https://help.galaxyproject.org/t/usegalaxy-org-account-activation-required-no-activation-email-received/18406)
**Author:** [@Yamini\_chandel](https://help.galaxyproject.org/u/Yamini_chandel)\ **Replies:** 1\ **Last updated:** [September 21, 2026, 6:44pm UTC](https://help.galaxyproject.org/t/usegalaxy-org-account-activation-required-no-activation-email-received/18406 "2026-09-21T18:44:47Z")
Hello Galaxy Support, I am using UseGalaxy.org and I am getting the error: “Action requires account activation.” I am already logged into my account and I have successfully completed several steps in my Galaxy history… --- ## [Revival of login bug](https://help.galaxyproject.org/t/revival-of-login-bug/18382)
**Author:** [@sukasuru](https://help.galaxyproject.org/u/sukasuru)\ **Replies:** 1\ **Last updated:** [September 14, 2026, 6:12pm UTC](https://help.galaxyproject.org/t/revival-of-login-bug/18382 "2026-09-14T18:12:13Z")
Hi, an issue last logged here in 2023 reemerged where upon trying to enter in the reset password link into my browser for the panel view, it defaults back to the login page. In fact the link isn’t being registered as a l… [Previous page](https://help.galaxyproject.org/latest.md) [Next page](https://help.galaxyproject.org/latest.md?page=2)