# Latest **URL:** https://help.galaxyproject.org/latest.md?page=4 [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) **Page:** 5 --- ## [Failure updating an IT for test.galaxyproject.org](https://help.galaxyproject.org/t/failure-updating-an-it-for-test-galaxyproject-org/17492)
**Author:** [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Replies:** 11\ **Last updated:** [July 7, 2026, 5:16pm UTC](https://help.galaxyproject.org/t/failure-updating-an-it-for-test-galaxyproject-org/17492 "2026-07-07T17:16:28Z")
I am trying to understand what the proper workflow is to update my IT to test on test.galaxyproject.org . The short story is that I update and push my Docker image (and new tag) for the IT to quay, then do a “shed\_update… --- ## [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… --- ## [ChiRa for Chimeric eClip data processing - Split ChiRa collapse out put as files to large processing](https://help.galaxyproject.org/t/chira-for-chimeric-eclip-data-processing-split-chira-collapse-out-put-as-files-to-large-processing/18097)
**Author:** [@S\_Staplet](https://help.galaxyproject.org/u/S_Staplet)\ **Replies:** 1\ **Last updated:** [July 6, 2026, 3:08am UTC](https://help.galaxyproject.org/t/chira-for-chimeric-eclip-data-processing-split-chira-collapse-out-put-as-files-to-large-processing/18097 "2026-07-06T03:08:34Z")
Hi there, I’m using the ChiRA workflow from "RNA-RNA interactome data analysis" transcriptomics tutorial. And I have had to split my ChiRa collapse output files into 500k read fasta files to enable mapping; as the orig… --- ## [DEseq2: Interpreting 3 or more factor levels](https://help.galaxyproject.org/t/deseq2-interpreting-3-or-more-factor-levels/18133)
**Author:** [@tbd](https://help.galaxyproject.org/u/tbd)\ **Replies:** 1\ **Last updated:** [July 6, 2026, 3:02am UTC](https://help.galaxyproject.org/t/deseq2-interpreting-3-or-more-factor-levels/18133 "2026-07-06T03:02:00Z")
Hello, I recently used DEseq2 to compare featureCounts output from 9 samples: 3 in each of 3 factor levels: Factor: Day Level 1: Day1 (samples 1, 2, 3) Level 2: Day2 (samples 4, 5, 6) Level 3 Day3 (samples 7, 8, 9) W… --- ## [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. --- ## [Lotus2 failing because it 'used more memory than it was allocated' but 90% of storage space is free](https://help.galaxyproject.org/t/lotus2-failing-because-it-used-more-memory-than-it-was-allocated-but-90-of-storage-space-is-free/18144)
**Author:** [@raphbow](https://help.galaxyproject.org/u/raphbow)\ **Replies:** 1\ **Last updated:** [July 6, 2026, 2:42am UTC](https://help.galaxyproject.org/t/lotus2-failing-because-it-used-more-memory-than-it-was-allocated-but-90-of-storage-space-is-free/18144 "2026-07-06T02:42:13Z")
Hi there, I am running the Lotus2 tool with multiple fastq files. When I include the whole dataset (27 fastq files) the job fails with the error message, ‘This job was terminated because it used more memory than it wa… --- ## [Do these data require trimming/preprocessing?](https://help.galaxyproject.org/t/do-these-data-require-trimming-preprocessing/18140)
**Author:** [@09303030076](https://help.galaxyproject.org/u/09303030076)\ **Replies:** 2\ **Last updated:** [July 5, 2026, 11:21am UTC](https://help.galaxyproject.org/t/do-these-data-require-trimming-preprocessing/18140 "2026-07-05T11:21:53Z")
Hi everyone I’m working with these samples in Galaxy and just generated this MultiQC report. Based on the status checks, I have a few questions: Do these data require trimming/preprocessing? Which tool would you recom… --- ## [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 … --- ## [InterProScan job running for 10 days on usegalaxy.eu – is this normal?](https://help.galaxyproject.org/t/interproscan-job-running-for-10-days-on-usegalaxy-eu-is-this-normal/18123)
**Author:** [@Santosh\_Lavhale](https://help.galaxyproject.org/u/Santosh_Lavhale)\ **Replies:** 2\ **Last updated:** [June 30, 2026, 4:31pm UTC](https://help.galaxyproject.org/t/interproscan-job-running-for-10-days-on-usegalaxy-eu-is-this-normal/18123 "2026-06-30T16:31:52Z")
Hello, I am running an InterProScan analysis, and my job has been running for about 10 days without completing. Here are some details: Tool: InterProScan Input: proteome dataset File size: ~50 MB (FASTA format/ .fa) R… --- ## [Gene synthesis oligo design](https://help.galaxyproject.org/t/gene-synthesis-oligo-design/13850)
**Author:** [@BenMulder](https://help.galaxyproject.org/u/BenMulder)\ **Replies:** 8\ **Last updated:** [June 30, 2026, 11:16am UTC](https://help.galaxyproject.org/t/gene-synthesis-oligo-design/13850 "2026-06-30T11:16:29Z")
Dear all, I’m trying to find a tool for invitro gene synthesis oligo design similar to DNAWorks which is discontinued in Biowulf. Galaxy is supposed to have Gene2Oligo, but I could not find it. I’m also concerned that… --- ## [Uploading FASTQ file to Galaxy](https://help.galaxyproject.org/t/uploading-fastq-file-to-galaxy/18120)
**Author:** [@Yutian\_Xia](https://help.galaxyproject.org/u/Yutian_Xia)\ **Replies:** 2\ **Last updated:** [June 29, 2026, 8:13pm UTC](https://help.galaxyproject.org/t/uploading-fastq-file-to-galaxy/18120 "2026-06-29T20:13:52Z")
Hello everyone, When I try to upload a FASTQ file to Galaxy for my homework, the progress bar goes from 0% to 100%, but after a few seconds, it drops back to 0% and starts over. This loop has been repeating for more tha… --- ## [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. --- ## [Snippy is taking over 24 hours to get started - is this normal (resolved)](https://help.galaxyproject.org/t/snippy-is-taking-over-24-hours-to-get-started-is-this-normal-resolved/18113)
**Author:** [@Ken\_Saville](https://help.galaxyproject.org/u/Ken_Saville)\ **Replies:** 1\ **Last updated:** [June 29, 2026, 2:09am UTC](https://help.galaxyproject.org/t/snippy-is-taking-over-24-hours-to-get-started-is-this-normal-resolved/18113 "2026-06-29T02:09:03Z")
Snippy is taking over 24 hours to get started - is this normal It runs on the .eu site but not .org Here’s a link to my history Snippy is taking over 24 hours to get started - is this normal --- ## [RNA STAR and Falco Down? (resolved)](https://help.galaxyproject.org/t/rna-star-and-falco-down-resolved/18118)
**Author:** [@09303030076](https://help.galaxyproject.org/u/09303030076)\ **Replies:** 1\ **Last updated:** [June 29, 2026, 2:06am UTC](https://help.galaxyproject.org/t/rna-star-and-falco-down-resolved/18118 "2026-06-29T02:06:08Z")
I got problem that Falco and rna-star tools is down, and it is already 36 h I am stuck in this --- ## [Errno 122: Disc quota exceeded error despite 15% storage usage on accunt (resolved)](https://help.galaxyproject.org/t/errno-122-disc-quota-exceeded-error-despite-15-storage-usage-on-accunt-resolved/18119)
**Author:** [@davielslocum](https://help.galaxyproject.org/u/davielslocum)\ **Replies:** 2\ **Last updated:** [June 29, 2026, 1:43am UTC](https://help.galaxyproject.org/t/errno-122-disc-quota-exceeded-error-despite-15-storage-usage-on-accunt-resolved/18119 "2026-06-29T01:43:23Z")
Despite using every troubleshooting method I can locate online, I am unable to stop this error from happening. From my understanding that means it’s more than likely a system error - but I don’t see any reported outag… --- ## [SortMeRNA outputting empty files](https://help.galaxyproject.org/t/sortmerna-outputting-empty-files/18102)
**Author:** [@vrm39](https://help.galaxyproject.org/u/vrm39)\ **Replies:** 3\ **Last updated:** [June 29, 2026, 1:30am UTC](https://help.galaxyproject.org/t/sortmerna-outputting-empty-files/18102 "2026-06-29T01:30:19Z")
I’m new to Galaxy, but I am trying to use SortMeRNA v 2.1b.6 to filter rRNA out of paired metagenome datasets. I am using default parameters, all available reference databases, paired-out, and I am including unaligned/re… --- ## [SRA reads into Galaxy: Study to Accessions](https://help.galaxyproject.org/t/sra-reads-into-galaxy-study-to-accessions/18108)
**Author:** [@Rambha\_Jha](https://help.galaxyproject.org/u/Rambha_Jha)\ **Replies:** 1\ **Last updated:** [June 25, 2026, 5:27pm UTC](https://help.galaxyproject.org/t/sra-reads-into-galaxy-study-to-accessions/18108 "2026-06-25T17:27:18Z")
PRJNA1096305 this is SRA datasets and i want to analyse this single cell data to identify the subsets of neutrophil. How will I do it I am new to RNA-sequencing analysis and have just started with a dataset but not able… --- ## [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… --- ## [Enhancement: STARsolo to support Velocyto (spliced/unspliced) matrices](https://help.galaxyproject.org/t/enhancement-starsolo-to-support-velocyto-spliced-unspliced-matrices/18035)
**Author:** [@100517cqmu](https://help.galaxyproject.org/u/100517cqmu)\ **Replies:** 2\ **Last updated:** [June 24, 2026, 9:55am UTC](https://help.galaxyproject.org/t/enhancement-starsolo-to-support-velocyto-spliced-unspliced-matrices/18035 "2026-06-24T09:55:02Z")
Describe the bug When running the RNA STARsolo tool on usegalaxy.org (tested on versions up to 2.7.11b+galaxy1 and 2.7.10b+galaxy4), the wrapper completely fails to export the Velocyto matrices (spliced.mtx, unspliced.m… --- ## [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… --- ## [Does using the same gtf file for RNA Star and featureCounts cause problems?](https://help.galaxyproject.org/t/does-using-the-same-gtf-file-for-rna-star-and-featurecounts-cause-problems/18094)
**Author:** [@artintz](https://help.galaxyproject.org/u/artintz)\ **Replies:** 1\ **Last updated:** [June 24, 2026, 2:15am UTC](https://help.galaxyproject.org/t/does-using-the-same-gtf-file-for-rna-star-and-featurecounts-cause-problems/18094 "2026-06-24T02:15:44Z")
Hello there, I my RNA-seq analysis in Galaxy, I aligned my reads using STAR with the UCSC hg38 reference genome (hg38.knownGene.gtf.gz ). After quantification with featurecounts and running DESeq2, My IDs were in UniPro… --- ## [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 … --- ## [Unable to run ITs; Galaxy could not be reached](https://help.galaxyproject.org/t/unable-to-run-its-galaxy-could-not-be-reached/18082)
**Author:** [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Replies:** 4\ **Last updated:** [June 23, 2026, 6:49am UTC](https://help.galaxyproject.org/t/unable-to-run-its-galaxy-could-not-be-reached/18082 "2026-06-23T06:49:01Z")
I’m currently unable to run ITs it seems. For JupyterLab or RStudio, I get: Galaxy could not be reached .You are seeing this message because a request to Galaxy timed out or was refused… For my IT, PhysiCell Studio, I … --- ## [HUMAnN Workflow Error](https://help.galaxyproject.org/t/humann-workflow-error/17281)
**Author:** [@zpho3nix](https://help.galaxyproject.org/u/zpho3nix)\ **Replies:** 3\ **Last updated:** [June 22, 2026, 2:49pm UTC](https://help.galaxyproject.org/t/humann-workflow-error/17281 "2026-06-22T14:49:56Z")
Hi, Please provide support troubleshooting this error. Here is a link to my workflow:Galaxy Thanks, BB --- ## [New Galaxy Tool: LC-MS Peak Picker (XCMS CentWave)](https://help.galaxyproject.org/t/new-galaxy-tool-lc-ms-peak-picker-xcms-centwave/18084)
**Author:** [@Hardik\_Sood](https://help.galaxyproject.org/u/Hardik_Sood)\ **Replies:** 0\ **Last updated:** [June 19, 2026, 12:04am UTC](https://help.galaxyproject.org/t/new-galaxy-tool-lc-ms-peak-picker-xcms-centwave/18084 "2026-06-19T00:04:40Z")
I’ve developed a Galaxy wrapper for the Bioconductor XCMS CentWave algorithm that enables peak detection on raw .mzML and .mzXML files without writing R code. Key Features: Industry-standard CentWave algorithm Batch p… --- ## [Kaiju database request](https://help.galaxyproject.org/t/kaiju-database-request/17748)
**Author:** [@chuanzhai](https://help.galaxyproject.org/u/chuanzhai)\ **Replies:** 13\ **Last updated:** [June 18, 2026, 6:17pm UTC](https://help.galaxyproject.org/t/kaiju-database-request/17748 "2026-06-18T18:17:10Z")
Dear Galaxy Team, I would like to run Kaiju using a reference database that includes bacteria, archaea, and eukaryotes, such as refseq\_nr. Could you please help add this database? Thank you! --- ## [MultiQC tool down?](https://help.galaxyproject.org/t/multiqc-tool-down/18068)
**Author:** [@mmnashrullah](https://help.galaxyproject.org/u/mmnashrullah)\ **Replies:** 2\ **Last updated:** [June 18, 2026, 4:09pm UTC](https://help.galaxyproject.org/t/multiqc-tool-down/18068 "2026-06-18T16:09:35Z")
Hi All, I got problem that MultiQC tool is down, and it is already 1 h I am stuck in this position. Link to the tool: https://usegalaxy.eu/?tool\_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmultiqc%2Fmultiqc%2F1.35%2Bgala… [Previous page](https://help.galaxyproject.org/latest.md?page=3) [Next page](https://help.galaxyproject.org/latest.md?page=5)