# Uncategorized **URL:** https://help.galaxyproject.org/c/uncategorized/1.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Fatal error with MetahplAn2](https://help.galaxyproject.org/t/fatal-error-with-metahplan2/18470)
**Author:** [@Nicolas\_Fierling](https://help.galaxyproject.org/u/Nicolas_Fierling)\ **Replies:** 1\ **Last updated:** [October 22, 2026, 12:17pm UTC](https://help.galaxyproject.org/t/fatal-error-with-metahplan2/18470 "2026-10-22T12:17:25Z")
Hello, I am encountering an issue with MetaPhlAn while processing my metagenomic data. I tried following the tutorial using the reference dataset provided, but I encountered the same problem. A fatal error occurs, stat… --- ## [Subject: Recover existing Galaxy Main Tool Shed account](https://help.galaxyproject.org/t/subject-recover-existing-galaxy-main-tool-shed-account/18509)
**Author:** [@diazlab](https://help.galaxyproject.org/u/diazlab)\ **Replies:** 1\ **Last updated:** [October 22, 2026, 12:36am UTC](https://help.galaxyproject.org/t/subject-recover-existing-galaxy-main-tool-shed-account/18509 "2026-10-22T00:36:49Z")
Hello Galaxy team, I’m preparing to publish SPICE to the Main Galaxy Tool Shed. My email address appears to be associated with an existing Main Tool Shed account, but I cannot log in. The password-reset option is not v… --- ## [Jobs stuck in "queued" state for hours on usegalaxy.org (Filtlong and Seqtk seq)](https://help.galaxyproject.org/t/jobs-stuck-in-queued-state-for-hours-on-usegalaxy-org-filtlong-and-seqtk-seq/18488)
**Author:** [@Julian\_Vasquez](https://help.galaxyproject.org/u/Julian_Vasquez)\ **Replies:** 3\ **Last updated:** [October 22, 2026, 12:22am UTC](https://help.galaxyproject.org/t/jobs-stuck-in-queued-state-for-hours-on-usegalaxy-org-filtlong-and-seqtk-seq/18488 "2026-10-22T00:22:02Z")
Hi everyone, I’m using galaxy .org and my jobs have been stuck in the “new / queued” state for more than 3 hours. Not a single job has started running. What I’m running: Filtlong on a collection of 128 Nanopore FAST… --- ## [Account activation required when uploading datasets](https://help.galaxyproject.org/t/account-activation-required-when-uploading-datasets/18520)
**Author:** [@Guilherme\_Martins\_de](https://help.galaxyproject.org/u/Guilherme_Martins_de)\ **Replies:** 1\ **Last updated:** [October 20, 2026, 2:14pm UTC](https://help.galaxyproject.org/t/account-activation-required-when-uploading-datasets/18520 "2026-10-20T14:14:59Z")
Hello Galaxy Europe team, I am able to log in to my account, but whenever I try to upload a dataset or run a tool, I receive the message: “Action requires account activation.” My storage usage is 0%, and I have tried t… --- ## [Storage quota increase request – account theo\_9800 (usegalaxy.fr)](https://help.galaxyproject.org/t/storage-quota-increase-request-account-theo-9800-usegalaxy-fr/18479)
**Author:** [@Theo](https://help.galaxyproject.org/u/Theo)\ **Replies:** 1\ **Last updated:** [October 17, 2026, 12:05am UTC](https://help.galaxyproject.org/t/storage-quota-increase-request-account-theo-9800-usegalaxy-fr/18479 "2026-10-17T00:05:09Z")
Hello, I’m a research engineer at the MetaToul-AXIOM metabolomics platform (INRAE Toxalim, Toulouse). I’m processing a large untargeted LC-MS dataset with XCMS-based tools on, and my current 100 GB quota is no longer en… --- ## [Prokka\_error\_message\_Argument “1.7.8” isn’t numeric in numeric 2026 edition](https://help.galaxyproject.org/t/prokka-error-message-argument-1-7-8-isn-t-numeric-in-numeric-2026-edition/18476)
**Author:** [@kmjones](https://help.galaxyproject.org/u/kmjones)\ **Replies:** 2\ **Last updated:** [October 16, 2026, 11:05pm UTC](https://help.galaxyproject.org/t/prokka-error-message-argument-1-7-8-isn-t-numeric-in-numeric-2026-edition/18476 "2026-10-16T23:05:41Z")
Prokka\_error\_message\_Argument “1.7.8” isn’t numeric in numeric 2026 edition I received the Prokka error message 'Argument “1.7.8” isn’t numeric lt (\<) at /usr/local/bin/prokka line 259 just like Ahmed\_Hammad in 2022.… --- ## [GTDB-TK version 2.4.0 included in my workflow due to a broken latest version 2.7.2 is expiring soon](https://help.galaxyproject.org/t/gtdb-tk-version-2-4-0-included-in-my-workflow-due-to-a-broken-latest-version-2-7-2-is-expiring-soon/18459)
**Author:** [@kafilattai1](https://help.galaxyproject.org/u/kafilattai1)\ **Replies:** 1\ **Last updated:** [October 15, 2026, 7:42pm UTC](https://help.galaxyproject.org/t/gtdb-tk-version-2-4-0-included-in-my-workflow-due-to-a-broken-latest-version-2-7-2-is-expiring-soon/18459 "2026-10-15T19:42:21Z")
The GTDB-TK version 2.4.0 included in my working because the latest version 2.7.2 was failing is expiring soon and the workflow is no longer working properly. Please what can I do to fix this? --- ## [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. --- ## [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. --- ## [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 --- ## [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,… --- ## [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… --- ## [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 --- ## [How to run VGP workflow with large files?](https://help.galaxyproject.org/t/how-to-run-vgp-workflow-with-large-files/18368)
**Author:** [@jinglin](https://help.galaxyproject.org/u/jinglin)\ **Replies:** 2\ **Last updated:** [September 9, 2026, 6:30am UTC](https://help.galaxyproject.org/t/how-to-run-vgp-workflow-with-large-files/18368 "2026-09-09T06:30:20Z")
I’m trying to run VGP workflow for my genome assembly, but my HiFi data is large which is 230GB. It is about 60GB in compressed (.gz) format, but VGP workflow only accept uncompressed files. My total storage size is only… --- ## [Prodigal Gene Predictor: error option (# Other genetic codes 1-25) stderr Invalid translation table specified](https://help.galaxyproject.org/t/prodigal-gene-predictor-error-option-other-genetic-codes-1-25-stderr-invalid-translation-table-specified/18350)
**Author:** [@tvtv195](https://help.galaxyproject.org/u/tvtv195)\ **Replies:** 1\ **Last updated:** [September 7, 2026, 5:55pm UTC](https://help.galaxyproject.org/t/prodigal-gene-predictor-error-option-other-genetic-codes-1-25-stderr-invalid-translation-table-specified/18350 "2026-09-07T17:55:12Z")
I am experiencing a bug in this specific version of the Galaxy wrapper (Galaxy Version 2.6.3+galaxy0). The developer forgot to link the conditional text field container to the # : Other genetic codes 1-25 selection choi… --- ## [Galaxy IT Physicell: execution troubleshooting](https://help.galaxyproject.org/t/galaxy-it-physicell-execution-troubleshooting/18367)
**Author:** [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Replies:** 2\ **Last updated:** [September 2, 2026, 6:12pm UTC](https://help.galaxyproject.org/t/galaxy-it-physicell-execution-troubleshooting/18367 "2026-09-02T18:12:43Z")
I seem to have a similar problem - my IT will not start. Here’s my shared History: Galaxy --- ## [How to structure design file for Deseq2 analysis on multiple factors](https://help.galaxyproject.org/t/how-to-structure-design-file-for-deseq2-analysis-on-multiple-factors/18353)
**Author:** [@Nadia2112](https://help.galaxyproject.org/u/Nadia2112)\ **Replies:** 1\ **Last updated:** [September 2, 2026, 7:01am UTC](https://help.galaxyproject.org/t/how-to-structure-design-file-for-deseq2-analysis-on-multiple-factors/18353 "2026-09-02T07:01:45Z")
After running KallistoQuant, I need to analyze my data on DeSeq2. The factors I have in my dataset are genotype (2 genotypes, WT and MUT) and treatment (3 treatments, R, L and V) and I would like to analyze them both sep… --- ## [IGV visualization fail](https://help.galaxyproject.org/t/igv-visualization-fail/18354)
**Author:** [@scholtz](https://help.galaxyproject.org/u/scholtz)\ **Replies:** 1\ **Last updated:** [August 31, 2026, 4:10pm UTC](https://help.galaxyproject.org/t/igv-visualization-fail/18354 "2026-08-31T16:10:52Z")
I tried to visualize my aligned files (merged bam, generated with RNA STAR) directly from Galaxy.eu with local IGV, but received the following warning from IGV: Error message: Unknown BAM index file type: null in null. N… --- ## [Reading old support threads — do you prefer follow-ups as new topics?](https://help.galaxyproject.org/t/reading-old-support-threads-do-you-prefer-follow-ups-as-new-topics/18335)
**Author:** [@roadtrip6587](https://help.galaxyproject.org/u/roadtrip6587)\ **Replies:** 3\ **Last updated:** [August 29, 2026, 1:36pm UTC](https://help.galaxyproject.org/t/reading-old-support-threads-do-you-prefer-follow-ups-as-new-topics/18335 "2026-08-29T13:36:18Z")
Hi everyone, relatively new here. I’ve been going through older threads while learning the platform and often find half-answered questions. Quick question about local habits: when an old topic is close to what I want to… --- ## [Request to update the Kraken2 microsporidia database (EuPathDB-46)](https://help.galaxyproject.org/t/request-to-update-the-kraken2-microsporidia-database-eupathdb-46/18341)
**Author:** [@Sing-P](https://help.galaxyproject.org/u/Sing-P)\ **Replies:** 1\ **Last updated:** [August 25, 2026, 3:34am UTC](https://help.galaxyproject.org/t/request-to-update-the-kraken2-microsporidia-database-eupathdb-46/18341 "2026-08-25T03:34:55Z")
I’m currently working on microsporidia genome analysis, and Kraken2 is an essential tool in my workflow. The microsporidia-specific Kraken2 database currently available is EuPathDB-46 (2023 version). Over the past 2–3 ye… --- ## [Repeated DATA\_FETCH failures affecting multiple FASTQ datasets](https://help.galaxyproject.org/t/repeated-data-fetch-failures-affecting-multiple-fastq-datasets/18302)
**Author:** [@rega](https://help.galaxyproject.org/u/rega)\ **Replies:** 1\ **Last updated:** [August 19, 2026, 7:47pm UTC](https://help.galaxyproject.org/t/repeated-data-fetch-failures-affecting-multiple-fastq-datasets/18302 "2026-08-19T19:47:41Z")
Dear Galaxy Support Team, I am experiencing repeated failures when uploading several datasets to Microbiology Galaxy (https://microbiology.usegalaxy.eu/). The problem first occurred with 36\_S36\_R1\_001.fastq.gz, which h… --- ## [HUMAnN Collection Mapping Launch Failure](https://help.galaxyproject.org/t/humann-collection-mapping-launch-failure/18290)
**Author:** [@Reki](https://help.galaxyproject.org/u/Reki)\ **Replies:** 1\ **Last updated:** [August 18, 2026, 5:50pm UTC](https://help.galaxyproject.org/t/humann-collection-mapping-launch-failure/18290 "2026-08-18T17:50:39Z")
HUMAnN 3.9 runs successfully on individual datasets using: Bowtie2 unaligned read pairs (collection 646) MetaPhlAn predicted taxon relative abundances (collection 945) bypass taxonomic profiling However, when selectin… [Next page](https://help.galaxyproject.org/c/uncategorized/1.md?page=1)