# Uncategorized **URL:** https://help.galaxyproject.org/c/uncategorized/1.md?page=2 [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) **Page:** 3 --- ## [GTDB-Tk Classify genomes error type 3](https://help.galaxyproject.org/t/gtdb-tk-classify-genomes-error-type-3/17736)
**Author:** [@Jesus\_Tapia](https://help.galaxyproject.org/u/Jesus_Tapia)\ **Replies:** 5\ **Last updated:** [July 13, 2026, 7:04pm UTC](https://help.galaxyproject.org/t/gtdb-tk-classify-genomes-error-type-3/17736 "2026-07-13T19:04:18Z")
error in GTDB-tk classifier usage: gtdbtk {de\_novo\_wf,classify\_wf,identify,align,infer,classify,root,decorate,infer\_ranks,ani\_rep,test,trim\_msa,remove\_labels,convert\_to\_itol,convert\_to\_species,export\_msa,c… --- ## [ AMRFinderPlus database configuration error on Galaxy Europe](https://help.galaxyproject.org/t/amrfinderplus-database-configuration-error-on-galaxy-europe/18154)
**Author:** [@carmen.sanchez](https://help.galaxyproject.org/u/carmen.sanchez)\ **Replies:** 1\ **Last updated:** [July 12, 2026, 12:09pm UTC](https://help.galaxyproject.org/t/amrfinderplus-database-configuration-error-on-galaxy-europe/18154 "2026-07-12T12:09:48Z")
Subject: AMRFinderPlus database configuration error on Galaxy Europe Hello, I am using AMRFinderPlus on usegalaxy.eu with the AMRFinder database V4.2-2026-05-15.1. Every job fails before the analysis starts with the f… --- ## [Errors during starting Galaxy on local server](https://help.galaxyproject.org/t/errors-during-starting-galaxy-on-local-server/18158)
**Author:** [@Charmax](https://help.galaxyproject.org/u/Charmax)\ **Replies:** 3\ **Last updated:** [July 10, 2026, 1:05pm UTC](https://help.galaxyproject.org/t/errors-during-starting-galaxy-on-local-server/18158 "2026-07-10T13:05:59Z")
I was trying to run galaxy on a server for around 1 week. However after I cloned the git repository and started “sh run.sh” directly, there were two error messages showing up: galaxy.tool\_util.toolbox.integrated\_panel… --- ## [Account activation required error on usegalaxy.org](https://help.galaxyproject.org/t/account-activation-required-error-on-usegalaxy-org/18125)
**Author:** [@Heba\_Hathout](https://help.galaxyproject.org/u/Heba_Hathout)\ **Replies:** 2\ **Last updated:** [July 10, 2026, 12:22am UTC](https://help.galaxyproject.org/t/account-activation-required-error-on-usegalaxy-org/18125 "2026-07-10T00:22:53Z")
Hello, I signed in with Google on usegalaxy dot org but I keep getting the message ’ Action requires account activation’ when trying to upload files. I never received an activation email. Please help activate my account,… --- ## [Can't upload history from galaxy.eu](https://help.galaxyproject.org/t/cant-upload-history-from-galaxy-eu/18115)
**Author:** [@Jon\_Colman](https://help.galaxyproject.org/u/Jon_Colman)\ **Replies:** 12\ **Last updated:** [July 9, 2026, 5:05am UTC](https://help.galaxyproject.org/t/cant-upload-history-from-galaxy-eu/18115 "2026-07-09T05:05:54Z")
Normally not a problem, though lately been extremely slow. Now all I get is an error when I try to upload to galaxy.org I tried copying link and pasting to galaxy.org, instant error. Tried copying history url and uploa… --- ## [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… --- ## [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 --- ## [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… --- ## [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… --- ## [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… --- ## [Metadata change stuck in orange](https://help.galaxyproject.org/t/metadata-change-stuck-in-orange/18059)
**Author:** [@Melanie\_Marlow](https://help.galaxyproject.org/u/Melanie_Marlow)\ **Replies:** 0\ **Last updated:** [June 15, 2026, 4:33pm UTC](https://help.galaxyproject.org/t/metadata-change-stuck-in-orange/18059 "2026-06-15T16:33:26Z")
Hi! I tried to change the metadata on a file but it is stuck on orange and “metadata is being auto-detected”. I want to cancel the job so I can try something else, but I am unable to get it to stop. I have tried deleting… --- ## [Removing mismatched bases](https://help.galaxyproject.org/t/removing-mismatched-bases/18026)
**Author:** [@cjain](https://help.galaxyproject.org/u/cjain)\ **Replies:** 1\ **Last updated:** [June 10, 2026, 3:22am UTC](https://help.galaxyproject.org/t/removing-mismatched-bases/18026 "2026-06-10T03:22:59Z")
While visualizing my alignments on IGV, I noticed that some of the reads contain mismatches at the 3’ end. Is there a way to generate an alignment file with the mismatches removed? Thanks! --- ## [Pavian, broken website](https://help.galaxyproject.org/t/pavian-broken-website/18016)
**Author:** [@brynn\_l](https://help.galaxyproject.org/u/brynn_l)\ **Replies:** 3\ **Last updated:** [June 8, 2026, 5:08pm UTC](https://help.galaxyproject.org/t/pavian-broken-website/18016 "2026-06-08T17:08:48Z")
It showed a broken website like the figure below, when I opened the Pavian interactive tool. I followed the tutorial and opened it as the job status turned orange. Thank you for your time. History:https://usegalaxy.org/… --- ## [Krakentools: Extract Kraken Reads By ID](https://help.galaxyproject.org/t/krakentools-extract-kraken-reads-by-id/18010)
**Author:** [@Zhenyu\_Shen](https://help.galaxyproject.org/u/Zhenyu_Shen)\ **Replies:** 1\ **Last updated:** [June 3, 2026, 8:38pm UTC](https://help.galaxyproject.org/t/krakentools-extract-kraken-reads-by-id/18010 "2026-06-03T20:38:41Z")
It seems the “Include children” and “Include parents” do not work for the resulting files of Kraken2 in the Gaxlaxy. --- ## [Snippy 4.6.0 contig-mode job intermittently fails with samtools sort -m 0M](https://help.galaxyproject.org/t/snippy-4-6-0-contig-mode-job-intermittently-fails-with-samtools-sort-m-0m/17759)
**Author:** [@dip](https://help.galaxyproject.org/u/dip)\ **Replies:** 1\ **Last updated:** [May 30, 2026, 6:35am UTC](https://help.galaxyproject.org/t/snippy-4-6-0-contig-mode-job-intermittently-fails-with-samtools-sort-m-0m/17759 "2026-05-30T06:35:37Z")
Hello Galaxy community, I am running Snippy 4.6.0 in Galaxy using assembled bacterial genome contigs as input. I am using contig mode with one FASTA genome as the reference and another assembled FASTA genome as the quer… --- ## [Long waiting times until metadata is set](https://help.galaxyproject.org/t/long-waiting-times-until-metadata-is-set/17752)
**Author:** [@casio](https://help.galaxyproject.org/u/casio)\ **Replies:** 4\ **Last updated:** [May 27, 2026, 6:03pm UTC](https://help.galaxyproject.org/t/long-waiting-times-until-metadata-is-set/17752 "2026-05-27T18:03:06Z")
Hi everyone, I am reaching out because I have hit a major performance wall with my Galaxy instance and could use some advice from the community. I am currently managing a 160 TB instance where the entire database and d… --- ## [Galaxy-main.usegalaxy.org is down?](https://help.galaxyproject.org/t/galaxy-main-usegalaxy-org-is-down/17751)
**Author:** [@Muniza\_123](https://help.galaxyproject.org/u/Muniza_123)\ **Replies:** 1\ **Last updated:** [May 26, 2026, 5:25pm UTC](https://help.galaxyproject.org/t/galaxy-main-usegalaxy-org-is-down/17751 "2026-05-26T17:25:03Z")
I am unable to access or reload my galaxy account since 12:00 PM today. is the US galaxy server really down or only i am getting this response??? Galaxy could not be reached You are seeing this message because a request… --- ## [Footprint tool help](https://help.galaxyproject.org/t/footprint-tool-help/17742)
**Author:** [@Mario\_Diaz](https://help.galaxyproject.org/u/Mario_Diaz)\ **Replies:** 1\ **Last updated:** [May 20, 2026, 7:32pm UTC](https://help.galaxyproject.org/t/footprint-tool-help/17742 "2026-05-20T19:32:23Z")
Hi, I’m trying to use footprint tool in Galaxy for ATAC-seq and I’m a bit confused about some of the required inputs. I understand that I need to provide: the aligned BAM file chromosome sizes motif coordinate… --- ## [Problem caused by the chromosome identifiers when using CustomProDB](https://help.galaxyproject.org/t/problem-caused-by-the-chromosome-identifiers-when-using-customprodb/17737)
**Author:** [@XinZhouUmea](https://help.galaxyproject.org/u/XinZhouUmea)\ **Replies:** 4\ **Last updated:** [May 20, 2026, 2:59pm UTC](https://help.galaxyproject.org/t/problem-caused-by-the-chromosome-identifiers-when-using-customprodb/17737 "2026-05-20T14:59:11Z")
Hi, I’m trying to use CustomProDB to create a protein fast file out of my transcriptomic variant data from rat (Rn6). The problem is that my bam file use chromosome identifiers like 1,3,2 …MT instead of chr1, chr2…chrM … --- ## [GALAXY Tool development](https://help.galaxyproject.org/t/galaxy-tool-development/17735)
**Author:** [@Mobile\_short\_film](https://help.galaxyproject.org/u/Mobile_short_film)\ **Replies:** 5\ **Last updated:** [May 19, 2026, 2:56pm UTC](https://help.galaxyproject.org/t/galaxy-tool-development/17735 "2026-05-19T14:56:31Z")
Hi I am wrapping a python script as GALAXY tool. But I am getting an error message. Please see the error message and suggest for the possible fix. --- ## [Extracting data from a .gff3 file](https://help.galaxyproject.org/t/extracting-data-from-a-gff3-file/17723)
**Author:** [@kate2](https://help.galaxyproject.org/u/kate2)\ **Replies:** 3\ **Last updated:** [May 18, 2026, 1:30pm UTC](https://help.galaxyproject.org/t/extracting-data-from-a-gff3-file/17723 "2026-05-18T13:30:45Z")
Afternoon, hopefully a simple question. I want to extract data from a .gff3 file and add it to the relevant gene id in a list of genes contained in a separate file, however the gene id in the .gff3 file is amongst other… --- ## [Problem retrieving data from Apollo](https://help.galaxyproject.org/t/problem-retrieving-data-from-apollo/17730)
**Author:** [@MonaSalem](https://help.galaxyproject.org/u/MonaSalem)\ **Replies:** 6\ **Last updated:** [May 13, 2026, 11:08pm UTC](https://help.galaxyproject.org/t/problem-retrieving-data-from-apollo/17730 "2026-05-13T23:08:31Z")
Hello, I have constantly used Galaxy to annotate some phage genomes. However, I have been trying to retrieve old data from Apollo into Galaxy for 3 weeks now with no success. I even uploaded the genome all over again, r… --- ## [Barcode Splitter fails consistently - 12K barcodes](https://help.galaxyproject.org/t/barcode-splitter-fails-consistently-12k-barcodes/17649)
**Author:** [@Yael\_Gershon](https://help.galaxyproject.org/u/Yael_Gershon)\ **Replies:** 5\ **Last updated:** [May 8, 2026, 8:25pm UTC](https://help.galaxyproject.org/t/barcode-splitter-fails-consistently-12k-barcodes/17649 "2026-05-08T20:25:44Z")
Hi, I’m using Barcode Splitter (v1.0.1) on usegalaxy.org but it fails every time with “Error: bad input file, expecting line with sequences”, “\>10000 output datasets”, and exit code 255. The setup includes a barcode fil… --- ## [Why my jobs are being queued for more than 24 hours and still waiting](https://help.galaxyproject.org/t/why-my-jobs-are-being-queued-for-more-than-24-hours-and-still-waiting/17708)
**Author:** [@vichetra\_sam](https://help.galaxyproject.org/u/vichetra_sam)\ **Replies:** 1\ **Last updated:** [May 6, 2026, 4:24pm UTC](https://help.galaxyproject.org/t/why-my-jobs-are-being-queued-for-more-than-24-hours-and-still-waiting/17708 "2026-05-06T16:24:50Z")
Hi I submitted a job more than 24 hours ago, and it is still waiting in a queue. I find it a bit unusual . How could I reach out the admin for help ? Regards. --- ## [KOfam database (HMM profiles of KEGG Orthologs): licensing and KEGG](https://help.galaxyproject.org/t/kofam-database-hmm-profiles-of-kegg-orthologs-licensing-and-kegg/17693)
**Author:** [@Pavithra\_Ramamurthy](https://help.galaxyproject.org/u/Pavithra_Ramamurthy)\ **Replies:** 1\ **Last updated:** [April 29, 2026, 7:27pm UTC](https://help.galaxyproject.org/t/kofam-database-hmm-profiles-of-kegg-orthologs-licensing-and-kegg/17693 "2026-04-29T19:27:32Z")
I am working on functional annotation workflows in Galaxy using KofamScan. Currently, the tool is available, but the KOfam database (HMM profiles of KEGG Orthologs) is not installed, so I cannot select a database when … --- ## [Kraken2 databases question](https://help.galaxyproject.org/t/kraken2-databases-question/17690)
**Author:** [@Pedro\_Fernandes\_de\_S](https://help.galaxyproject.org/u/Pedro_Fernandes_de_S)\ **Replies:** 1\ **Last updated:** [April 29, 2026, 7:06pm UTC](https://help.galaxyproject.org/t/kraken2-databases-question/17690 "2026-04-29T19:06:14Z")
Can someone explain to me what are the kraken2 databases, like, what they have? i havent found it anywhere --- ## [Samtools index not visible in galaxy](https://help.galaxyproject.org/t/samtools-index-not-visible-in-galaxy/17691)
**Author:** [@Alberto\_Alberti](https://help.galaxyproject.org/u/Alberto_Alberti)\ **Replies:** 1\ **Last updated:** [April 29, 2026, 1:33pm UTC](https://help.galaxyproject.org/t/samtools-index-not-visible-in-galaxy/17691 "2026-04-29T13:33:38Z")
please anyone can help? i can not find samtools index anywhere in my galaxy europe! --- ## [Unfold bug, missing newline char](https://help.galaxyproject.org/t/unfold-bug-missing-newline-char/17687)
**Author:** [@Alper\_Yilmaz](https://help.galaxyproject.org/u/Alper_Yilmaz)\ **Replies:** 3\ **Last updated:** [April 27, 2026, 7:36pm UTC](https://help.galaxyproject.org/t/unfold-bug-missing-newline-char/17687 "2026-04-27T19:36:37Z")
I’m having a problem with unfold tool. I uploaded this file to galaxy and used unfold. gene kegg gene1 map1,map2 gene2 - gene3 map1,map2,map3 I was expecting to have this format: gene1 map1 gene1 map2 … --- ## [Bacteria community and Antibiotic Resistance Gene](https://help.galaxyproject.org/t/bacteria-community-and-antibiotic-resistance-gene/17670)
**Author:** [@santatra](https://help.galaxyproject.org/u/santatra)\ **Replies:** 1\ **Last updated:** [April 22, 2026, 6:11pm UTC](https://help.galaxyproject.org/t/bacteria-community-and-antibiotic-resistance-gene/17670 "2026-04-22T18:11:21Z")
Hello everyone, I am working on metagenomic data from human samples (oral swabs) and I would appreciate guidance on how to properly analyze and integrate two outputs generated in Galaxy. I have: 1. Bacterial taxonomy … [Previous page](https://help.galaxyproject.org/c/uncategorized/1.md?page=1) [Next page](https://help.galaxyproject.org/c/uncategorized/1.md?page=3)