# Latest **URL:** https://help.galaxyproject.org/latest.md?no_subcategories=false&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 --- ## [STARsolo custom reference fails during genomeGenerate — need genomeChrBinNbits for fragmented Nicotiana genome](https://help.galaxyproject.org/t/starsolo-custom-reference-fails-during-genomegenerate-need-genomechrbinnbits-for-fragmented-nicotiana-genome/18360)
**Author:** [@fforn](https://help.galaxyproject.org/u/fforn)\ **Replies:** 4\ **Last updated:** [September 3, 2026, 6:53pm UTC](https://help.galaxyproject.org/t/starsolo-custom-reference-fails-during-genomegenerate-need-genomechrbinnbits-for-fragmented-nicotiana-genome/18360 "2026-09-03T18:53:22Z")
Hi Galaxy Europe team, I am trying to reconstruct a published 10x Genomics v3 single-nucleus RNA-seq dataset from Nicotiana tabacum K326 using RNA STARsolo on singlecell.usegalaxy.eu. Tool: RNA STARsolo 2.7.11b+galaxy2 … --- ## [Dorado now missing from usegalaxy.eu site...?](https://help.galaxyproject.org/t/dorado-now-missing-from-usegalaxy-eu-site/18352)
**Author:** [@scyllas1981](https://help.galaxyproject.org/u/scyllas1981)\ **Replies:** 4\ **Last updated:** [September 3, 2026, 1:55am UTC](https://help.galaxyproject.org/t/dorado-now-missing-from-usegalaxy-eu-site/18352 "2026-09-03T01:55:48Z")
Hi all - hoping an admin usegalaxy.e.u could help Today I can’t seem to find dorado in the tools - has it been removed??? Have used recently, this seems a significant change if removed. Thanks Graham --- ## [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 --- ## [File remain greyed out](https://help.galaxyproject.org/t/file-remain-greyed-out/16505)
**Author:** [@Nadya](https://help.galaxyproject.org/u/Nadya)\ **Replies:** 1\ **Last updated:** [November 19, 2025, 9:51pm UTC](https://help.galaxyproject.org/t/file-remain-greyed-out/16505 "2025-11-19T21:51:00Z")
Hello, Galaxy was working fine for me for several hours, but after I uploaded another relatively small file, it has remained greyed out for hours. Is there anything I can do to get it working again, or are there any iss… --- ## [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… --- ## [Gromacs exceeded 60h](https://help.galaxyproject.org/t/gromacs-exceeded-60h/18363)
**Author:** [@Turki](https://help.galaxyproject.org/u/Turki)\ **Replies:** 0\ **Last updated:** [August 31, 2026, 3:22pm UTC](https://help.galaxyproject.org/t/gromacs-exceeded-60h/18363 "2026-08-31T15:22:22Z")
Hello, I have a GROMACS 2022+galaxy0 molecular dynamics job on usegalaxy.eu using GPU resources. The job has been in the running state for approximately 60 hours. Standard output and standard error are empty, and the int… --- ## [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… --- ## [Pre.cluster (mothur) empty outputs: consider using groups! Please see tutorial example](https://help.galaxyproject.org/t/pre-cluster-mothur-empty-outputs-consider-using-groups-please-see-tutorial-example/18347)
**Author:** [@Heba\_Hathout](https://help.galaxyproject.org/u/Heba_Hathout)\ **Replies:** 1\ **Last updated:** [August 27, 2026, 4:27pm UTC](https://help.galaxyproject.org/t/pre-cluster-mothur-empty-outputs-consider-using-groups-please-see-tutorial-example/18347 "2026-08-27T16:27:53Z")
Server URL: usegalaxy dot org I’m running the Pre.cluster tool (mothur, Galaxy Version 1.39.5.0) on a 16S mothur pipeline (23 samples, RedSeaSeawater\_16S\_Mothur pipeline history). The job has been stuck in “running” s… --- ## [NOVOplasty new version](https://help.galaxyproject.org/t/novoplasty-new-version/18314)
**Author:** [@M\_gras](https://help.galaxyproject.org/u/M_gras)\ **Replies:** 4\ **Last updated:** [August 26, 2026, 10:27am UTC](https://help.galaxyproject.org/t/novoplasty-new-version/18314 "2026-08-26T10:27:50Z")
Hello, I use NOVOplasty for mitogenome assembly. For one assembly I need the option " Reduce ambiguous N’s " and it’s available with the version 4.3.3 Is it possible to add the version please ??? Thank you very much M… --- ## [Jobs stuck in 'new' state — Faster Download and Extract Reads in FASTQ](https://help.galaxyproject.org/t/jobs-stuck-in-new-state-faster-download-and-extract-reads-in-fastq/18337)
**Author:** [@Ghaida](https://help.galaxyproject.org/u/Ghaida)\ **Replies:** 4\ **Last updated:** [August 25, 2026, 12:12pm UTC](https://help.galaxyproject.org/t/jobs-stuck-in-new-state-faster-download-and-extract-reads-in-fastq/18337 "2026-08-25T12:12:55Z")
Resolved :white\_check\_mark: Tool name: “Faster Download and Extract Reads in FASTQ format from NCBI SRA (Galaxy Version 3.1.1+galaxy1)” Clicking Run Tool shows ‘please wait’ for under a second, then reverts with no job… --- ## [RStudio interactive tool doesn't load, seemingly because of http/https mix](https://help.galaxyproject.org/t/rstudio-interactive-tool-doesnt-load-seemingly-because-of-http-https-mix/18294)
**Author:** [@Peter\_van\_Heusden](https://help.galaxyproject.org/u/Peter_van_Heusden)\ **Replies:** 2\ **Last updated:** [August 25, 2026, 11:47am UTC](https://help.galaxyproject.org/t/rstudio-interactive-tool-doesnt-load-seemingly-because-of-http-https-mix/18294 "2026-08-25T11:47:48Z")
Hi there When I try and get a RStudio session I get a blank page that seems to result from the interactive tool being linked to via http instead of https: Loading the url with https works. Is this a config error on … --- ## [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… --- ## [Immediate error when running RNA STAR](https://help.galaxyproject.org/t/immediate-error-when-running-rna-star/18319)
**Author:** [@knmcfarland](https://help.galaxyproject.org/u/knmcfarland)\ **Replies:** 2\ **Last updated:** [August 25, 2026, 3:31am UTC](https://help.galaxyproject.org/t/immediate-error-when-running-rna-star/18319 "2026-08-25T03:31:02Z")
Hi! I’m trying to align fastq files to the built in mouse genome (GRCm39/mm39) using RNA STAR. I am getting errors of “Encountered an unhandled exception while caching job destination dynamic rule” almost immediately or … --- ## [Usegalaxy.eu HUMAnN 3.9+galaxy1 fails because ChocoPhlAn directory contains mixed database versions](https://help.galaxyproject.org/t/usegalaxy-eu-humann-3-9-galaxy1-fails-because-chocophlan-directory-contains-mixed-database-versions/18339)
**Author:** [@Hc\_G](https://help.galaxyproject.org/u/Hc_G)\ **Replies:** 1\ **Last updated:** [August 25, 2026, 3:29am UTC](https://help.galaxyproject.org/t/usegalaxy-eu-humann-3-9-galaxy1-fails-because-chocophlan-directory-contains-mixed-database-versions/18339 "2026-08-25T03:29:16Z")
Hello Galaxy team, I am running HUMAnN on usegalaxy.eu and encountered the same ChocoPhlAn version error reported in this previous topic: https://help.galaxyproject.org/t/humann-fails-due-to-metaphlan-database-mismatch… --- ## [RStudio Interactive Tool cannot be launched](https://help.galaxyproject.org/t/rstudio-interactive-tool-cannot-be-launched/18304)
**Author:** [@luzihao](https://help.galaxyproject.org/u/luzihao)\ **Replies:** 5\ **Last updated:** [August 24, 2026, 11:15am UTC](https://help.galaxyproject.org/t/rstudio-interactive-tool-cannot-be-launched/18304 "2026-08-24T11:15:11Z")
Hello Galaxy support team, I am trying to use the RStudio Interactive Tool in Galaxy, but I have been unable to open it for approximately one month. When I launch RStudio from the Interactive Tools section, the job sta… --- ## [Uploading Fastq.gz is very slow](https://help.galaxyproject.org/t/uploading-fastq-gz-is-very-slow/18315)
**Author:** [@Yanzi](https://help.galaxyproject.org/u/Yanzi)\ **Replies:** 3\ **Last updated:** [August 24, 2026, 9:02am UTC](https://help.galaxyproject.org/t/uploading-fastq-gz-is-very-slow/18315 "2026-08-24T09:02:33Z")
Hi, I want to upload some fastq.gz files to eu server, together 180G size. But the uploading speed is very slow, which normally is very fast from my previous experience. I can’t finish upload one file (8Gb) in 2 hours. I… --- ## [Featurecounts error with reference GTF file](https://help.galaxyproject.org/t/featurecounts-error-with-reference-gtf-file/18311)
**Author:** [@Xxl](https://help.galaxyproject.org/u/Xxl)\ **Replies:** 1\ **Last updated:** [August 24, 2026, 1:09am UTC](https://help.galaxyproject.org/t/featurecounts-error-with-reference-gtf-file/18311 "2026-08-24T01:09:58Z")
Hi, I’m troubleshooting an RNA-seq analysis in Galaxy and am running into an error at the featureCounts step. I am analyzing Xenopus laevis RNA-seq data and uploaded both the reference genome FASTA file and the correspo… --- ## [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… --- ## [GTDB-Tk jobs remaining queued for several days on usegalaxy.eu](https://help.galaxyproject.org/t/gtdb-tk-jobs-remaining-queued-for-several-days-on-usegalaxy-eu/18291)
**Author:** [@Raul\_Carlos\_Mainar\_J](https://help.galaxyproject.org/u/Raul_Carlos_Mainar_J)\ **Replies:** 4\ **Last updated:** [August 19, 2026, 8:58am UTC](https://help.galaxyproject.org/t/gtdb-tk-jobs-remaining-queued-for-several-days-on-usegalaxy-eu/18291 "2026-08-19T08:58:15Z")
Hello, I am running a MAG analysis workflow on Galaxy Europe and I currently have several GTDB-Tk Classify genomes jobs that have remained in queued state for several days. I am using: Galaxy Europe (usegalaxy.eu) GT… --- ## [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… --- ## [Job delays at UseGalaxy.eu Aug 18 2026: Resolved, please leave queued jobs queued + rerun errors](https://help.galaxyproject.org/t/job-delays-at-usegalaxy-eu-aug-18-2026-resolved-please-leave-queued-jobs-queued-rerun-errors/18292)
**Author:** [@Jon\_Colman](https://help.galaxyproject.org/u/Jon_Colman)\ **Replies:** 2\ **Last updated:** [August 18, 2026, 4:06pm UTC](https://help.galaxyproject.org/t/job-delays-at-usegalaxy-eu-aug-18-2026-resolved-please-leave-queued-jobs-queued-rerun-errors/18292 "2026-08-18T16:06:08Z")
Bowtie2 isn’t working. I tried using a normal workflow, and it immediately turns red. So I tried making a new workflow with newest version, still turns red without running. "Unable to run job due to misconfiguration … --- ## [GALAXY/ BRIDGE failure submitting job](https://help.galaxyproject.org/t/galaxy-bridge-failure-submitting-job/18288)
**Author:** [@zineddine](https://help.galaxyproject.org/u/zineddine)\ **Replies:** 1\ **Last updated:** [August 18, 2026, 4:12am UTC](https://help.galaxyproject.org/t/galaxy-bridge-failure-submitting-job/18288 "2026-08-18T04:12:03Z")
I’m having some problems using ‘Gromacs Initial Setup’; the task isn’t being submitted, even when I switch web browsers , and the same message appears when using ‘Get PDB’ – and the same may well apply to all the other … --- ## [Galaxy france log in issue](https://help.galaxyproject.org/t/galaxy-france-log-in-issue/18287)
**Author:** [@abul](https://help.galaxyproject.org/u/abul)\ **Replies:** 1\ **Last updated:** [August 18, 2026, 3:58am UTC](https://help.galaxyproject.org/t/galaxy-france-log-in-issue/18287 "2026-08-18T03:58:49Z")
Subject: Workflow4Metabolomics Galaxy login page stuck on Loading Dear Workflow4Metabolomics team, I have been unable to access the Workflow4Metabolomics Galaxy server for the past two days. When I open the login page,… --- ## [HUMAnN error version](https://help.galaxyproject.org/t/humann-error-version/18284)
**Author:** [@Reki](https://help.galaxyproject.org/u/Reki)\ **Replies:** 1\ **Last updated:** [August 14, 2026, 8:10pm UTC](https://help.galaxyproject.org/t/humann-error-version/18284 "2026-08-14T20:10:44Z")
Galaxy Microbiology HUMAnN 3.9+galaxy1 Error: "The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJun23" The only MetaPhlAn marker database available under “Locally cache… --- ## [miRNA seq differential analysis](https://help.galaxyproject.org/t/mirna-seq-differential-analysis/4326)
**Author:** [@Mayur\_Doke](https://help.galaxyproject.org/u/Mayur_Doke)\ **Replies:** 1\ **Last updated:** [August 14, 2026, 7:25pm UTC](https://help.galaxyproject.org/t/mirna-seq-differential-analysis/4326 "2026-08-14T19:25:02Z")
Hello, I am writing to ask your help in regard to performing differential analysis to analyze miR RNA-seq data in https://usegalaxy.eu/ . I have miRNA seq data and I have analyzed in the following way- Initial QC - re… --- ## [Help ChewBBACA: using collection folders and NormalizeFasta to avoid "ValueError: This FASTA file contains comments "](https://help.galaxyproject.org/t/help-chewbbaca-using-collection-folders-and-normalizefasta-to-avoid-valueerror-this-fasta-file-contains-comments/18278)
**Author:** [@msuh](https://help.galaxyproject.org/u/msuh)\ **Replies:** 5\ **Last updated:** [August 13, 2026, 7:43pm UTC](https://help.galaxyproject.org/t/help-chewbbaca-using-collection-folders-and-normalizefasta-to-avoid-valueerror-this-fasta-file-contains-comments/18278 "2026-08-13T19:43:15Z")
I am working through a training module (Step-by-step Tutorial - chewBBACA 3.5.4 documentation) using datasets provided. Whenever I input cgMLSTschema95.txt file as genes-list to do “Allele calling with additional genome… --- ## [Inconsistency between storage listed in "Preferred Galaxy Storage" and in "Storage overview by location"](https://help.galaxyproject.org/t/inconsistency-between-storage-listed-in-preferred-galaxy-storage-and-in-storage-overview-by-location/18279)
**Author:** [@Peter\_van\_Heusden](https://help.galaxyproject.org/u/Peter_van_Heusden)\ **Replies:** 3\ **Last updated:** [August 13, 2026, 8:33am UTC](https://help.galaxyproject.org/t/inconsistency-between-storage-listed-in-preferred-galaxy-storage-and-in-storage-overview-by-location/18279 "2026-08-13T08:33:30Z")
On usegalaxy.eu when I use the “Storage overview by location” interface I get this view: i.e. many object stores such as “files33” and “files30” along with my main (user defined) “backblaze\_b2” object storage. When … --- ## [SPAdes queued for hours](https://help.galaxyproject.org/t/spades-queued-for-hours/18280)
**Author:** [@Chris\_Tsoukas](https://help.galaxyproject.org/u/Chris_Tsoukas)\ **Replies:** 1\ **Last updated:** [August 12, 2026, 11:28pm UTC](https://help.galaxyproject.org/t/spades-queued-for-hours/18280 "2026-08-12T23:28:26Z")
Hi! I am trying to run SPAdes in Galaxy Europe, and the jobs are in queue for hours without starting. Is there anything I can do? Thanks in advance. --- ## [Jobs stuck after deleting and purging mid-run](https://help.galaxyproject.org/t/jobs-stuck-after-deleting-and-purging-mid-run/18274)
**Author:** [@Raghini\_Rajaram](https://help.galaxyproject.org/u/Raghini_Rajaram)\ **Replies:** 7\ **Last updated:** [August 12, 2026, 11:18pm UTC](https://help.galaxyproject.org/t/jobs-stuck-after-deleting-and-purging-mid-run/18274 "2026-08-12T23:18:34Z")
Hi, I deleted a few jobs while they were running and also purged them. But they still seem to be running and I am not able to run any new jobs (they are staying grey). Could the admin manually clear the stuck jobs? My … [Previous page](https://help.galaxyproject.org/latest.md?no_subcategories=false) [Next page](https://help.galaxyproject.org/latest.md?no_subcategories=false&page=2)