# usegalaxy.eu support **URL:** https://help.galaxyproject.org/c/usegalaxy-eu-support/6.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 --- ## [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. --- ## ["Invalid storage location" when trying to move data to Backblaze B2](https://help.galaxyproject.org/t/invalid-storage-location-when-trying-to-move-data-to-backblaze-b2/18276)
**Author:** [@Peter\_van\_Heusden](https://help.galaxyproject.org/u/Peter_van_Heusden)\ **Replies:** 5\ **Last updated:** [August 12, 2026, 10:30am UTC](https://help.galaxyproject.org/t/invalid-storage-location-when-trying-to-move-data-to-backblaze-b2/18276 "2026-08-12T10:30:55Z")
I’m trying to move the datasets in a history (8228344521d4e949) to my Backblaze B2 storage but when I try and do this with the “Manage storage location” option, I get told that “The selected storage location is not avail… --- ## [Notebooks: more about memory resources and HTP analysis](https://help.galaxyproject.org/t/notebooks-more-about-memory-resources-and-htp-analysis/18267)
**Author:** [@0808](https://help.galaxyproject.org/u/0808)\ **Replies:** 2\ **Last updated:** [August 11, 2026, 7:31am UTC](https://help.galaxyproject.org/t/notebooks-more-about-memory-resources-and-htp-analysis/18267 "2026-08-11T07:31:33Z")
Title: Request for higher-memory resource for RSEM v1.3.1 due to OOM Hello Galaxy Europe Support Team, I am reprocessing the public PRJEB40416 gastric cancer RNA-seq dataset on usegalaxy.eu. STAR alignment has comple… --- ## [GTDB-Tk, reference data, and job queues: leave jobs queued for this competitive cluster group!](https://help.galaxyproject.org/t/gtdb-tk-reference-data-and-job-queues-leave-jobs-queued-for-this-competitive-cluster-group/18237)
**Author:** [@horikini](https://help.galaxyproject.org/u/horikini)\ **Replies:** 3\ **Last updated:** [August 10, 2026, 6:21pm UTC](https://help.galaxyproject.org/t/gtdb-tk-reference-data-and-job-queues-leave-jobs-queued-for-this-competitive-cluster-group/18237 "2026-08-10T18:21:52Z")
Hi, I have a GTDB-Tk classify\_wf job that has been stuck in “queued” state (never transitioned to “running”) for over 73 hours. Job ID: 4838ba20a6d86765aad1b932f8f80dd1 Tool: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk\_cl… --- ## [Jobs remain in "new" state since Tuesday maintenance on usegalaxy.eu](https://help.galaxyproject.org/t/jobs-remain-in-new-state-since-tuesday-maintenance-on-usegalaxy-eu/18249)
**Author:** [@ehmig](https://help.galaxyproject.org/u/ehmig)\ **Replies:** 1\ **Last updated:** [August 6, 2026, 4:59pm UTC](https://help.galaxyproject.org/t/jobs-remain-in-new-state-since-tuesday-maintenance-on-usegalaxy-eu/18249 "2026-08-06T16:59:01Z")
Hello, I’m experiencing an issue on usegalaxy.eu since the scheduled maintenance on Tuesday at around 14:00 (CEST). Before the maintenance, everything was working normally. Since then, I have not been able to run any j… --- ## [Abnormally long-running BRAKER3 job on usegalaxy.eu](https://help.galaxyproject.org/t/abnormally-long-running-braker3-job-on-usegalaxy-eu/18244)
**Author:** [@lupolk](https://help.galaxyproject.org/u/lupolk)\ **Replies:** 2\ **Last updated:** [August 6, 2026, 2:32pm UTC](https://help.galaxyproject.org/t/abnormally-long-running-braker3-job-on-usegalaxy-eu/18244 "2026-08-06T14:32:06Z")
Hi, I have a BRAKER3 3.0.8+galaxy2 job that has been running since 14 July 2026. A previous submission of the same analysis remained running for more around a month until I cancelled it. Comparable BRAKER3 analyses for … --- ## [Jobs waiting to run](https://help.galaxyproject.org/t/jobs-waiting-to-run/9623)
**Author:** [@christkr08](https://help.galaxyproject.org/u/christkr08)\ **Replies:** 8\ **Last updated:** [June 4, 2023, 2:22pm UTC](https://help.galaxyproject.org/t/jobs-waiting-to-run/9623 "2023-06-04T14:22:51Z")
Hi all, I have uploaded my WGS fq.gz files yesterday but they are still waiting to run… Anyone else with similar problems or with any suggestion? Thanks for any help. --- ## [Datamash across many columns](https://help.galaxyproject.org/t/datamash-across-many-columns/18240)
**Author:** [@rmassei](https://help.galaxyproject.org/u/rmassei)\ **Replies:** 1\ **Last updated:** [August 5, 2026, 8:49pm UTC](https://help.galaxyproject.org/t/datamash-across-many-columns/18240 "2026-08-05T20:49:28Z")
Hi! I’m trying to group by a column and compute the median and mean per group across many columns of a CSV file. Datamash seems like the tool for this task, but it looks like I can only select a single column to perfor… --- ## [Issue Using MIBiG with BiG-SCAPE on Galaxy](https://help.galaxyproject.org/t/issue-using-mibig-with-big-scape-on-galaxy/18099)
**Author:** [@Shreyash\_04](https://help.galaxyproject.org/u/Shreyash_04)\ **Replies:** 3\ **Last updated:** [July 31, 2026, 7:35pm UTC](https://help.galaxyproject.org/t/issue-using-mibig-with-big-scape-on-galaxy/18099 "2026-07-31T19:35:11Z")
Dear Galaxy Support Team, I hope you are doing well. I am experiencing persistent issues while running BiG-SCAPE on Galaxy, specifically related to the inclusion of the MIBiG reference dataset. :red\_circle: MIBiG issu… --- ## [Interactive tools not working](https://help.galaxyproject.org/t/interactive-tools-not-working/18225)
**Author:** [@Chris\_Tsoukas](https://help.galaxyproject.org/u/Chris_Tsoukas)\ **Replies:** 1\ **Last updated:** [July 31, 2026, 10:36am UTC](https://help.galaxyproject.org/t/interactive-tools-not-working/18225 "2026-07-31T10:36:56Z")
Hello! I was using the JupyTool interactive tool and it worked pefectly. All of a sudden, when I am trying to load a previous notebook, or even start a new session, the three jobs are in queue (gray color, says this job … --- ## [MrBayes consensus tree file not shown in output](https://help.galaxyproject.org/t/mrbayes-consensus-tree-file-not-shown-in-output/18221)
**Author:** [@tavovato](https://help.galaxyproject.org/u/tavovato)\ **Replies:** 2\ **Last updated:** [July 30, 2026, 9:52pm UTC](https://help.galaxyproject.org/t/mrbayes-consensus-tree-file-not-shown-in-output/18221 "2026-07-30T21:52:26Z")
Hi! I ran a MrBayes analysis on usegalaxy.eu and the job seems to have completed successfully. The summary report indicates that several MrBayes output files were generated, including .run1.t, .run2.t, .pstat, .tstat, .… --- ## [MrBayes - no output files found](https://help.galaxyproject.org/t/mrbayes-no-output-files-found/16275)
**Author:** [@Alan\_Thomas](https://help.galaxyproject.org/u/Alan_Thomas)\ **Replies:** 4\ **Last updated:** [July 30, 2026, 6:12pm UTC](https://help.galaxyproject.org/t/mrbayes-no-output-files-found/16275 "2026-07-30T18:12:31Z")
Hai After analysing data using MrBayes in https://usegalaxy.eu/, output files are not created. No output files found. Only a text file was found. Could you please help me? Thank you. --- ## [Bioconductor packages failing to install in Galaxy Europe Interactive R (cannot access repository index)](https://help.galaxyproject.org/t/bioconductor-packages-failing-to-install-in-galaxy-europe-interactive-r-cannot-access-repository-index/18086)
**Author:** [@noor\_ali](https://help.galaxyproject.org/u/noor_ali)\ **Replies:** 1\ **Last updated:** [July 28, 2026, 9:15pm UTC](https://help.galaxyproject.org/t/bioconductor-packages-failing-to-install-in-galaxy-europe-interactive-r-cannot-access-repository-index/18086 "2026-07-28T21:15:01Z")
Hello everyone, I am currently using the Galaxy Europe Interactive R environment for a single-cell RNA-seq analysis workflow, but I am running into a persistent issue when trying to install Bioconductor packages. Probl… --- ## [Is image correlation in GALAXY possible while preserving aspect ratio (no distortion only rotation/scaling)?](https://help.galaxyproject.org/t/is-image-correlation-in-galaxy-possible-while-preserving-aspect-ratio-no-distortion-only-rotation-scaling/18114)
**Author:** [@Norbert\_Feuerechse](https://help.galaxyproject.org/u/Norbert_Feuerechse)\ **Replies:** 1\ **Last updated:** [July 28, 2026, 9:00pm UTC](https://help.galaxyproject.org/t/is-image-correlation-in-galaxy-possible-while-preserving-aspect-ratio-no-distortion-only-rotation-scaling/18114 "2026-07-28T21:00:17Z")
Hello Galaxy team, I would like to perform image correlation in GALAXY EU while allowing translation, rotation, and uniform scaling, but preventing any aspect ratio distortion (i.e., no non-uniform scaling or shear). T… --- ## [How to separate genomic from subgenomic RNA reads of Coronavirus?](https://help.galaxyproject.org/t/how-to-separate-genomic-from-subgenomic-rna-reads-of-coronavirus/18064)
**Author:** [@gi3547](https://help.galaxyproject.org/u/gi3547)\ **Replies:** 6\ **Last updated:** [July 27, 2026, 6:41pm UTC](https://help.galaxyproject.org/t/how-to-separate-genomic-from-subgenomic-rna-reads-of-coronavirus/18064 "2026-07-27T18:41:45Z")
Hello Everyone, I am a beginner Galaxy user, I sequenced total RNA of Coronavirus-infected huh-7 cells. First i filtered the human genome. Then mapped the rest of the reads. The problem is: there are reads belong to bot… --- ## [Invocation ID in RO-Crate](https://help.galaxyproject.org/t/invocation-id-in-ro-crate/18190)
**Author:** [@LauLauThom](https://help.galaxyproject.org/u/LauLauThom)\ **Replies:** 0\ **Last updated:** [July 20, 2026, 3:07pm UTC](https://help.galaxyproject.org/t/invocation-id-in-ro-crate/18190 "2026-07-20T15:07:05Z")
Hi there, I am using the Workflow Run RO-Crate export feature of galaxy to ingest workflow invocations in our internal data-management system (LabID). I would like to also save the link to these invocations together wi… --- ## [Galaxy server/UI pagination bug](https://help.galaxyproject.org/t/galaxy-server-ui-pagination-bug/18175)
**Author:** [@12Benne](https://help.galaxyproject.org/u/12Benne)\ **Replies:** 5\ **Last updated:** [July 20, 2026, 3:02pm UTC](https://help.galaxyproject.org/t/galaxy-server-ui-pagination-bug/18175 "2026-07-20T15:02:23Z")
I’m encountering a non-tool specific bug with drop down lists. Tool collection selector loads only the 50 most recent eligible datasets. Running a job increases the count from 107 to 108, displays the new output, and re… --- ## [Frozen Export History to File Source](https://help.galaxyproject.org/t/frozen-export-history-to-file-source/18168)
**Author:** [@LukaDM](https://help.galaxyproject.org/u/LukaDM)\ **Replies:** 1\ **Last updated:** [July 15, 2026, 7:42pm UTC](https://help.galaxyproject.org/t/frozen-export-history-to-file-source/18168 "2026-07-15T19:42:19Z")
Hello: I started exporting a 1.43 gb file using the tar.gz option with download link; it has been running for 5 hours. I would like to cancel it and re-start, but I don’t see that option. Do I have to just let it time-o… --- ## [TGS-GapCloser Node mount error](https://help.galaxyproject.org/t/tgs-gapcloser-node-mount-error/18160)
**Author:** [@Rui\_Alves](https://help.galaxyproject.org/u/Rui_Alves)\ **Replies:** 2\ **Last updated:** [July 13, 2026, 6:44am UTC](https://help.galaxyproject.org/t/tgs-gapcloser-node-mount-error/18160 "2026-07-13T06:44:38Z")
Hi, I am using TGS-Gapcloser to try and close the gaps in an assembly, providing fasta for hifi long reads. I am using galaxy. It does not work. The error message is as follows: FATAL: While checking container encr… --- ## [Current implementation of GTDB-Tk Classify genomes is broken (wrong default arguments)](https://help.galaxyproject.org/t/current-implementation-of-gtdb-tk-classify-genomes-is-broken-wrong-default-arguments/18057)
**Author:** [@jvollme](https://help.galaxyproject.org/u/jvollme)\ **Replies:** 1\ **Last updated:** [July 12, 2026, 11:09am UTC](https://help.galaxyproject.org/t/current-implementation-of-gtdb-tk-classify-genomes-is-broken-wrong-default-arguments/18057 "2026-07-12T11:09:20Z")
It appears the current toolshed implementations version 2.7.1 and 2.7.2 on usegalaxy.eu are broken? It appears they are still trying to use the default argument “skip\_ani\_screen”, which however is deprecated since versio… --- ## [Uploading issues ( fasta, faa, gbff files)](https://help.galaxyproject.org/t/uploading-issues-fasta-faa-gbff-files/18147)
**Author:** [@davide\_bersanetti](https://help.galaxyproject.org/u/davide_bersanetti)\ **Replies:** 1\ **Last updated:** [July 7, 2026, 1:58am UTC](https://help.galaxyproject.org/t/uploading-issues-fasta-faa-gbff-files/18147 "2026-07-07T01:58:59Z")
Morning Everyone, in our lab we are noticing problems with uploading data in Galaxy.eu, any news on what could be the cause ? Best, DB --- ## [Msconvert job failing on usegalaxy.org with Wine/disk quota errors](https://help.galaxyproject.org/t/msconvert-job-failing-on-usegalaxy-org-with-wine-disk-quota-errors/18126)
**Author:** [@Rasika\_Rathnayake](https://help.galaxyproject.org/u/Rasika_Rathnayake)\ **Replies:** 3\ **Last updated:** [July 6, 2026, 6:43pm UTC](https://help.galaxyproject.org/t/msconvert-job-failing-on-usegalaxy-org-with-wine-disk-quota-errors/18126 "2026-07-06T18:43:13Z")
Hello, I am following the Galaxy DIA/OpenSWATH proteomics tutorial and running msconvert. The job first failed with: wineserver: /tmp/.wine-0 is not owned by you After rerunning one file, it failed with: \[Errno 122\] D… --- ## [How to set the reference level in DESeq2 for treatment vs control comparison?](https://help.galaxyproject.org/t/how-to-set-the-reference-level-in-deseq2-for-treatment-vs-control-comparison/18128)
**Author:** [@09303030076](https://help.galaxyproject.org/u/09303030076)\ **Replies:** 1\ **Last updated:** [July 6, 2026, 2:52am UTC](https://help.galaxyproject.org/t/how-to-set-the-reference-level-in-deseq2-for-treatment-vs-control-comparison/18128 "2026-07-06T02:52:56Z")
Hello, Dear I would like to ask whether the first factor in DESeq2 should be set as the control or the treatment when the goal is to evaluate the changes in the treatment compared to the control. --- ## [Bowtie2 Galaxy Version 2.5.3+galaxy1: Data set colection](https://help.galaxyproject.org/t/bowtie2-galaxy-version-2-5-3-galaxy1-data-set-colection/18141)
**Author:** [@Rowan](https://help.galaxyproject.org/u/Rowan)\ **Replies:** 1\ **Last updated:** [July 3, 2026, 10:00am UTC](https://help.galaxyproject.org/t/bowtie2-galaxy-version-2-5-3-galaxy1-data-set-colection/18141 "2026-07-03T10:00:35Z")
Hi, I would like to ask. I have nested dataset colection and I was doing Bowtie2 Galaxy Version 2.5.3+galaxy1: Data set colection. Now, there is no such option in newest version. I tried to run it with similar results +… --- ## [Input tabular data into a Galaxy tool - Preserving row order](https://help.galaxyproject.org/t/input-tabular-data-into-a-galaxy-tool-preserving-row-order/18136)
**Author:** [@rmassei](https://help.galaxyproject.org/u/rmassei)\ **Replies:** 2\ **Last updated:** [July 2, 2026, 9:48am UTC](https://help.galaxyproject.org/t/input-tabular-data-into-a-galaxy-tool-preserving-row-order/18136 "2026-07-02T09:48:11Z")
HI! I am trying to inject a series of values sequentially into a tool so that it performs different cropping operations on an image. I have a tabular file that contains the following data: Column 1 Column 2 Column … --- ## [Kaiju2table unable to open files from a Kaiju output dataset collection](https://help.galaxyproject.org/t/kaiju2table-unable-to-open-files-from-a-kaiju-output-dataset-collection/18083)
**Author:** [@slghose](https://help.galaxyproject.org/u/slghose)\ **Replies:** 2\ **Last updated:** [June 29, 2026, 2:45pm UTC](https://help.galaxyproject.org/t/kaiju2table-unable-to-open-files-from-a-kaiju-output-dataset-collection/18083 "2026-06-29T14:45:23Z")
I am trying to run kaiju2table on a dataset collection output from Kaiju, which I ran on a collection of paired read files. Kaiju2table failed with the message that an error occurred with this dataset. The error was: “co… --- ## [Panaroo: GFF files in a Collection? Toggle option to retain file extensions in element sample identifiers](https://help.galaxyproject.org/t/panaroo-gff-files-in-a-collection-toggle-option-to-retain-file-extensions-in-element-sample-identifiers/18011)
**Author:** [@Ph\_c\_Mai](https://help.galaxyproject.org/u/Ph_c_Mai)\ **Replies:** 12\ **Last updated:** [June 29, 2026, 9:09am UTC](https://help.galaxyproject.org/t/panaroo-gff-files-in-a-collection-toggle-option-to-retain-file-extensions-in-element-sample-identifiers/18011 "2026-06-29T09:09:55Z")
My files of bacterial genomes are gff type, whose names all end with .gff. But I can’t run Panaroo with them. How can I run Panaroo with them? Thank you so much. --- ## [Slow downloading](https://help.galaxyproject.org/t/slow-downloading/18029)
**Author:** [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)\ **Replies:** 16\ **Last updated:** [June 24, 2026, 4:43pm UTC](https://help.galaxyproject.org/t/slow-downloading/18029 "2026-06-24T16:43:13Z")
Hello, I am trying to download BAM files from my usegalaxy.eu history, but the rate is \<20 KB/s. An internet speed test shows no problem with my connection. Could there be an issue on the server side? Note: I am located… --- ## [Recognizing paired collection for deep arg in galaxy europe server](https://help.galaxyproject.org/t/recognizing-paired-collection-for-deep-arg-in-galaxy-europe-server/18076)
**Author:** [@Varnika\_D](https://help.galaxyproject.org/u/Varnika_D)\ **Replies:** 1\ **Last updated:** [June 24, 2026, 2:52am UTC](https://help.galaxyproject.org/t/recognizing-paired-collection-for-deep-arg-in-galaxy-europe-server/18076 "2026-06-24T02:52:02Z")
I transferred Bowtie2 unaligned read pairs (fastqsanger.gz) from the us site to Europe site by exporting and importing a history. I built a paired collection but DeepARG short reads says ‘No compatible dataset pair datas… --- ## [TargetFinder score cutoff seems ignored; tool always behaves as cutoff 4](https://help.galaxyproject.org/t/targetfinder-score-cutoff-seems-ignored-tool-always-behaves-as-cutoff-4/18046)
**Author:** [@Martin\_Bartas](https://help.galaxyproject.org/u/Martin_Bartas)\ **Replies:** 3\ **Last updated:** [June 23, 2026, 9:16am UTC](https://help.galaxyproject.org/t/targetfinder-score-cutoff-seems-ignored-tool-always-behaves-as-cutoff-4/18046 "2026-06-23T09:16:18Z")
Hi Galaxy team, I am using the TargetFinder tool for plant small RNA target prediction (Galaxy tool version: 1.7.0+galaxy1). I may have found a possible issue with the Prediction score cutoff value parameter. In the … [Previous page](https://help.galaxyproject.org/c/usegalaxy-eu-support/6.md) [Next page](https://help.galaxyproject.org/c/usegalaxy-eu-support/6.md?page=2)