# usegalaxy.org support **URL:** https://help.galaxyproject.org/c/usegalaxy-org-support/5.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 --- ## [Trinotate running Error](https://help.galaxyproject.org/t/trinotate-running-error/5890)
**Author:** [@Akhil\_Velluva](https://help.galaxyproject.org/u/Akhil_Velluva)\ **Replies:** 3\ **Last updated:** [April 8, 2026, 2:10am UTC](https://help.galaxyproject.org/t/trinotate-running-error/5890 "2026-04-08T02:10:36Z")
I was running Trinotate and got error as like this Error, cannot locate version database file. Be sure it’s in your current directory. at /cvmfs/main.galaxyproject.org/deps/\_conda/envs/mulled-v1-d301214ea0391aec86b2f63… --- ## [Project help...(variant analysis)](https://help.galaxyproject.org/t/project-help-variant-analysis/3853)
**Author:** [@karp05](https://help.galaxyproject.org/u/karp05)\ **Replies:** 2\ **Last updated:** [April 8, 2026, 1:41am UTC](https://help.galaxyproject.org/t/project-help-variant-analysis/3853 "2026-04-08T01:41:53Z")
Hi, (note: I am an absolute complete beginner in this) Ive recently been taking a course on coursera about using galaxy and I have a project whereby I have to "Create a Galaxy workflow to identify polymorphic sites in … --- ## [Need help with selecting reference genome in Galaxy installed locally](https://help.galaxyproject.org/t/need-help-with-selecting-reference-genome-in-galaxy-installed-locally/4931)
**Author:** [@manojmw](https://help.galaxyproject.org/u/manojmw)\ **Replies:** 3\ **Last updated:** [April 8, 2026, 1:41am UTC](https://help.galaxyproject.org/t/need-help-with-selecting-reference-genome-in-galaxy-installed-locally/4931 "2026-04-08T01:41:17Z")
Hello everyone, I am trying to annotate a VCF file containing the sample data to predict the genes with polymorphic sites. I am using ANNOVAR tool. But, no options are available for me under Gene/Annotation/Databases in… --- ## [Annotate VCF with gene names](https://help.galaxyproject.org/t/annotate-vcf-with-gene-names/3153)
**Author:** [@yahia.elshabrawy](https://help.galaxyproject.org/u/yahia.elshabrawy)\ **Replies:** 4\ **Last updated:** [April 8, 2026, 1:40am UTC](https://help.galaxyproject.org/t/annotate-vcf-with-gene-names/3153 "2026-04-08T01:40:46Z")
Im trying to add annotations to a vcf file. I had paired-end reads of 3 individuals, I aligned each pair to the human hg19 genome, then I generated the VCF file using FreeBayes to call for variants of the 3 sets of data… --- ## [Unable to use 'ANNOVAR Annotate VCF' to annotate my vcf file](https://help.galaxyproject.org/t/unable-to-use-annovar-annotate-vcf-to-annotate-my-vcf-file/6431)
**Author:** [@Abieskawa](https://help.galaxyproject.org/u/Abieskawa)\ **Replies:** 2\ **Last updated:** [April 8, 2026, 1:38am UTC](https://help.galaxyproject.org/t/unable-to-use-annovar-annotate-vcf-to-annotate-my-vcf-file/6431 "2026-04-08T01:38:55Z")
Hello everyone. I want to annotate my vcf file and transfer it to tabular, so I can count the gene that content mutation maximum in number. When I use ANNOVAR Annotate VCF to annotate my vcf file, I cannot choose the ann… --- ## [ANNOVAR 0 lines result](https://help.galaxyproject.org/t/annovar-0-lines-result/2969)
**Author:** [@ThibautMatis](https://help.galaxyproject.org/u/ThibautMatis)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 1:38am UTC](https://help.galaxyproject.org/t/annovar-0-lines-result/2969 "2026-04-08T01:38:01Z")
Hi, I’m a beginner on Galaxy and I’m trying to use ANNOVAR on VCF files from exome (it’s all I have). Variant caller used was Samtool. VCF files have been mapped on hg19, and I filled this information when I imported my … --- ## [Annovar on galaxy v0.2 not working](https://help.galaxyproject.org/t/annovar-on-galaxy-v0-2-not-working/6796)
**Author:** [@aradhna](https://help.galaxyproject.org/u/aradhna)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 1:36am UTC](https://help.galaxyproject.org/t/annovar-on-galaxy-v0-2-not-working/6796 "2026-04-08T01:36:44Z")
Hello, I have to finish a project for an online course where I need to identify DNA polymorphic sites through galaxy. I want to annotate vcf file generated after free Bayes step. I am new to this analysis part and I hav… --- ## [Modifying text in a file](https://help.galaxyproject.org/t/modifying-text-in-a-file/4315)
**Author:** [@mich1213](https://help.galaxyproject.org/u/mich1213)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 1:08am UTC](https://help.galaxyproject.org/t/modifying-text-in-a-file/4315 "2026-04-08T01:08:30Z")
Hello, I am having some trouble with annotating my ID with Sailfish. I used Mouse gene mm10 (version 6) for my Sailfish. The error that I had with annotatemyID is same as below: Error in .testForValidKeys(x, keys, keyty… --- ## [Compute an expression on every row tool](https://help.galaxyproject.org/t/compute-an-expression-on-every-row-tool/4804)
**Author:** [@stauntok](https://help.galaxyproject.org/u/stauntok)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 12:37am UTC](https://help.galaxyproject.org/t/compute-an-expression-on-every-row-tool/4804 "2026-04-08T00:37:35Z")
When I use the tool Compute an expression on every row it does not include positions with a read depth of zero. How can I include these positions? --- ## [Troubleshooting paused jobs](https://help.galaxyproject.org/t/troubleshooting-paused-jobs/2123)
**Author:** [@Simon\_Mcglynn](https://help.galaxyproject.org/u/Simon_Mcglynn)\ **Replies:** 3\ **Last updated:** [April 8, 2026, 12:01am UTC](https://help.galaxyproject.org/t/troubleshooting-paused-jobs/2123 "2026-04-08T00:01:42Z")
I was uploading a few datasets but I forgot to log in and quickly went over disk quota, I logged in and began uploading once more. Once I was done I’d a quick scroll through to make sure everything was alright and found … --- ## [Negative disc quota](https://help.galaxyproject.org/t/negative-disc-quota/585)
**Author:** [@amaliaharrington](https://help.galaxyproject.org/u/amaliaharrington)\ **Replies:** 4\ **Last updated:** [April 7, 2026, 11:59pm UTC](https://help.galaxyproject.org/t/negative-disc-quota/585 "2026-04-07T23:59:31Z")
Hello, I currently have about 111GB of data that I have loaded to my account, but it says I have a negative quota of -346 GB (-138% of quota). When I delete items the number becomes more negative, when I add files it be… --- ## [Unregistered vs registered accounts in Galaxy](https://help.galaxyproject.org/t/unregistered-vs-registered-accounts-in-galaxy/4024)
**Author:** [@Eric\_Karofsky](https://help.galaxyproject.org/u/Eric_Karofsky)\ **Replies:** 2\ **Last updated:** [April 7, 2026, 11:53pm UTC](https://help.galaxyproject.org/t/unregistered-vs-registered-accounts-in-galaxy/4024 "2026-04-07T23:53:51Z")
What is the difference between using Galaxy as an unregistered user and a registered user ie, limited functionality? is there a limit on the unregistered access of compute or storage, or anything else? Thank you. --- ## [Disk Quota Not Refreshing](https://help.galaxyproject.org/t/disk-quota-not-refreshing/11858)
**Author:** [@SehajR](https://help.galaxyproject.org/u/SehajR)\ **Replies:** 4\ **Last updated:** [April 7, 2026, 10:22pm UTC](https://help.galaxyproject.org/t/disk-quota-not-refreshing/11858 "2026-04-07T22:22:45Z")
I am having an issue with my disk quota on the Main Galaxy server (250 GB). I had purged many datasets from my history (currently only have one history), but it has not updated the disk quota since yesterday. It shows th… --- ## [Search Data Libraries Datasets](https://help.galaxyproject.org/t/search-data-libraries-datasets/2755)
**Author:** [@Thahmina](https://help.galaxyproject.org/u/Thahmina)\ **Replies:** 1\ **Last updated:** [April 7, 2026, 9:52pm UTC](https://help.galaxyproject.org/t/search-data-libraries-datasets/2755 "2026-04-07T21:52:27Z")
Greetings, I know that searching on data library names and descriptions is possible, but I am trying to find the feature that enables the ability to search on names, descriptions or attributes of data library datasets. … --- ## [Add new version of reference genome: Tribolium castaneum (red flour beetle) Tcas5.2](https://help.galaxyproject.org/t/add-new-version-of-reference-genome-tribolium-castaneum-red-flour-beetle-tcas5-2/963)
**Author:** [@yoshitomoyasu](https://help.galaxyproject.org/u/yoshitomoyasu)\ **Replies:** 3\ **Last updated:** [April 7, 2026, 9:50pm UTC](https://help.galaxyproject.org/t/add-new-version-of-reference-genome-tribolium-castaneum-red-flour-beetle-tcas5-2/963 "2026-04-07T21:50:26Z")
Could you add the latest version of the Tribolium castaneum genome assembly (Tcas5.2) to the list? https://www.ncbi.nlm.nih.gov/genome?term=tribolium%20castaneum Thanks!! --- ## [View Button on Reads](https://help.galaxyproject.org/t/view-button-on-reads/17629)
**Author:** [@Jon\_Colman](https://help.galaxyproject.org/u/Jon_Colman)\ **Replies:** 8\ **Last updated:** [April 7, 2026, 7:42pm UTC](https://help.galaxyproject.org/t/view-button-on-reads/17629 "2026-04-07T19:42:29Z")
I noticed with the recent update with usegalaxy.org and now usegalaxy.eu, when I click on the view button to visually see a portion of the reads, the format has changed. Very much unreadable at this point. When I asse… --- ## [Mapping of Ambiguous Multi Mapping DNA Reads](https://help.galaxyproject.org/t/mapping-of-ambiguous-multi-mapping-dna-reads/17632)
**Author:** [@Jon\_Colman](https://help.galaxyproject.org/u/Jon_Colman)\ **Replies:** 6\ **Last updated:** [April 7, 2026, 2:24am UTC](https://help.galaxyproject.org/t/mapping-of-ambiguous-multi-mapping-dna-reads/17632 "2026-04-07T02:24:33Z")
I have been having difficulty mapping some eukaryotic species. I hadn’t thought of this issue until now. The species have relatively high similarity to humans with lots of ambiguous regions. I had thought because I wa… --- ## [Missing Gene trees in orthofinder outputs](https://help.galaxyproject.org/t/missing-gene-trees-in-orthofinder-outputs/17612)
**Author:** [@valeriolollo](https://help.galaxyproject.org/u/valeriolollo)\ **Replies:** 6\ **Last updated:** [April 1, 2026, 7:53pm UTC](https://help.galaxyproject.org/t/missing-gene-trees-in-orthofinder-outputs/17612 "2026-04-01T19:53:16Z")
Hi! I’m working on orthofinder 2.5.5+ and I’m having difficulties with the gene trees outcome. The error says “problem building datasets for collection”. While reading the help section I’ve noticed this line that says: … --- ## [Error in RNA STAR - wrong read ID line format](https://help.galaxyproject.org/t/error-in-rna-star-wrong-read-id-line-format/17599)
**Author:** [@AEJ](https://help.galaxyproject.org/u/AEJ)\ **Replies:** 2\ **Last updated:** [April 1, 2026, 6:11pm UTC](https://help.galaxyproject.org/t/error-in-rna-star-wrong-read-id-line-format/17599 "2026-04-01T18:11:31Z")
When running samples on RNA STAR, 15/16 samples ran perfectly with no errors. One sample returned the following fatal error: I can see that it’s an issue with the input file, but I’m lost as to how to address this. T… --- ## [Cannot run an IT tool: PhysiCell Studio](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899)
**Author:** [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Replies:** 17\ **Last updated:** [March 31, 2026, 6:18pm UTC](https://help.galaxyproject.org/t/cannot-run-an-it-tool-physicell-studio/16899 "2026-03-31T18:18:55Z")
Are there any known issues with usegalaxy.org running Interactive Tools today? I’ve been unable to run PhysiCell Studio, as well as the JupyterLab Notebook. I didn’t see any notices of downtime on the main page. I can, h… --- ## [Troubleshooting: Action requires account activation](https://help.galaxyproject.org/t/troubleshooting-action-requires-account-activation/17546)
**Author:** [@reman.sh.19](https://help.galaxyproject.org/u/reman.sh.19)\ **Replies:** 4\ **Last updated:** [March 23, 2026, 9:56pm UTC](https://help.galaxyproject.org/t/troubleshooting-action-requires-account-activation/17546 "2026-03-23T21:56:15Z")
Hello, I get the error “Action requires account activation” when submitting a job. Could you please activate my account? Thank you. --- ## [ExomeDepth Column gene](https://help.galaxyproject.org/t/exomedepth-column-gene/10117)
**Author:** [@egarzon](https://help.galaxyproject.org/u/egarzon)\ **Replies:** 1\ **Last updated:** [May 24, 2023, 6:14pm UTC](https://help.galaxyproject.org/t/exomedepth-column-gene/10117 "2023-05-24T18:14:48Z")
Hello, I have tried to run ExomeDepth from galaxy but the generated output does not indicate column 2 of the gene and I am unable to graph the results, thanks for your help --- ## [Workflow extraction issue](https://help.galaxyproject.org/t/workflow-extraction-issue/187)
**Author:** [@hov](https://help.galaxyproject.org/u/hov)\ **Replies:** 11\ **Last updated:** [March 20, 2026, 4:51pm UTC](https://help.galaxyproject.org/t/workflow-extraction-issue/187 "2026-03-20T16:51:23Z")
Hi all, I am trying to extract workflow from history, but Galaxy generates error, how can I overcome it? Error text is below. # Internal Server Error ## Galaxy was unable to successfully complete your request An err… --- ## [Encountered locale error when running edgeR](https://help.galaxyproject.org/t/encountered-locale-error-when-running-edger/17588)
**Author:** [@nickn](https://help.galaxyproject.org/u/nickn)\ **Replies:** 1\ **Last updated:** [March 19, 2026, 7:06am UTC](https://help.galaxyproject.org/t/encountered-locale-error-when-running-edger/17588 "2026-03-19T07:06:37Z")
I was able to run edgeR tool successfully last week. It normally takes about 2 minutes to complete but this time it ran for about 24 hrs and then gave this error. Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger… --- ## [Galaxy Loading Super Slow](https://help.galaxyproject.org/t/galaxy-loading-super-slow/17582)
**Author:** [@kabrooks2](https://help.galaxyproject.org/u/kabrooks2)\ **Replies:** 4\ **Last updated:** [March 17, 2026, 9:50pm UTC](https://help.galaxyproject.org/t/galaxy-loading-super-slow/17582 "2026-03-17T21:50:38Z")
Hi, I’m trying to purge my datasets and retrieve new ones, but everything is moving very slowly. I was also able to run one of my datasets, but the job has been stuck for three days. Is there anything I can do to fix th… --- ## [Download genome into Galaxy](https://help.galaxyproject.org/t/download-genome-into-galaxy/1884)
**Author:** [@Thend](https://help.galaxyproject.org/u/Thend)\ **Replies:** 10\ **Last updated:** [March 17, 2026, 6:06am UTC](https://help.galaxyproject.org/t/download-genome-into-galaxy/1884 "2026-03-17T06:06:04Z")
Dear All, Briefly, I would like to download a species genome (CBVK0000000000.1 Picea abies :: NCBI) into Galaxy. However, the fasta of the full genome of the species in many pieces (32). I have tried Getdata/Collection… --- ## [Need help running snippy for bacterial genome](https://help.galaxyproject.org/t/need-help-running-snippy-for-bacterial-genome/17572)
**Author:** [@Sudipta\_Talukder](https://help.galaxyproject.org/u/Sudipta_Talukder)\ **Replies:** 2\ **Last updated:** [March 17, 2026, 2:34am UTC](https://help.galaxyproject.org/t/need-help-running-snippy-for-bacterial-genome/17572 "2026-03-17T02:34:11Z")
I am running snippy for the E. coli sequences using one of my isolates as reference. Was able to do some but for some getting this error “ Fatal error: Exit code 2 ()”. I’d appreciate any suggestions. Possible cause it … --- ## [Problem with Helixer](https://help.galaxyproject.org/t/problem-with-helixer/17577)
**Author:** [@davidjoly](https://help.galaxyproject.org/u/davidjoly)\ **Replies:** 2\ **Last updated:** [March 16, 2026, 6:42pm UTC](https://help.galaxyproject.org/t/problem-with-helixer/17577 "2026-03-16T18:42:06Z")
I am trying to run Helixer on a 5 Mb sequence (which corresponds to a specific region from a chromosome I’m interested in). I obtain this error: Traceback (most recent call last): File "/usr/local/bin/fetc… --- ## [Cannot connect to Galaxy](https://help.galaxyproject.org/t/cannot-connect-to-galaxy/6293)
**Author:** [@Silvia](https://help.galaxyproject.org/u/Silvia)\ **Replies:** 6\ **Last updated:** [August 28, 2025, 7:17pm UTC](https://help.galaxyproject.org/t/cannot-connect-to-galaxy/6293 "2025-08-28T19:17:58Z")
hello all. I have a problem. I am trying to run stacks de novo without refrence genome for paired end reads. it run once, i tryied to download the results but one of the files kept saying corrupted. so I deleted the re… --- ## [What is up with the new update? So many tools stopped working](https://help.galaxyproject.org/t/what-is-up-with-the-new-update-so-many-tools-stopped-working/17553)
**Author:** [@bross39](https://help.galaxyproject.org/u/bross39)\ **Replies:** 1\ **Last updated:** [March 9, 2026, 4:16pm UTC](https://help.galaxyproject.org/t/what-is-up-with-the-new-update-so-many-tools-stopped-working/17553 "2026-03-09T16:16:56Z")
I teach a class with galaxy but this semester we are having lost of issues. We are having to revert to pervious versions of snippy, bowtie, featureCounts, etc. uploading SRA datavia the two tools is failing regularly. [Previous page](https://help.galaxyproject.org/c/usegalaxy-org-support/5.md?page=1) [Next page](https://help.galaxyproject.org/c/usegalaxy-org-support/5.md?page=3)