# usegalaxy.org support **URL:** https://help.galaxyproject.org/c/usegalaxy-org-support/5.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 --- ## [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 … --- ## [File Transfer VERY SLOW](https://help.galaxyproject.org/t/file-transfer-very-slow/18037)
**Author:** [@Jon\_Colman](https://help.galaxyproject.org/u/Jon_Colman)\ **Replies:** 7\ **Last updated:** [June 12, 2026, 11:18pm UTC](https://help.galaxyproject.org/t/file-transfer-very-slow/18037 "2026-06-12T23:18:28Z")
Trying to move some files from Galaxy.eu to Galaxy.org, going extremely slow or not moving at all. --- ## [featureCount; Fatal error: Exit code 255()](https://help.galaxyproject.org/t/featurecount-fatal-error-exit-code-255/18024)
**Author:** [@kitchia96](https://help.galaxyproject.org/u/kitchia96)\ **Replies:** 4\ **Last updated:** [June 12, 2026, 7:37pm UTC](https://help.galaxyproject.org/t/featurecount-fatal-error-exit-code-255/18024 "2026-06-12T19:37:06Z")
Hi I recently used the featureCount to quantitate aligned reads from STAR. And, I have faced this similar error code. According to AI, it seems to be suggesting that this might be due to its incompability of the current … --- ## [Account quota refresh and self-serve extended data scratch space storage](https://help.galaxyproject.org/t/account-quota-refresh-and-self-serve-extended-data-scratch-space-storage/18049)
**Author:** [@sepide](https://help.galaxyproject.org/u/sepide)\ **Replies:** 1\ **Last updated:** [June 12, 2026, 7:22pm UTC](https://help.galaxyproject.org/t/account-quota-refresh-and-self-serve-extended-data-scratch-space-storage/18049 "2026-06-12T19:22:18Z")
I have deleted my datasets and tried to purge them, but my quota is still showing as full --- ## [How can I improve very low assigned rate in featureCounts?](https://help.galaxyproject.org/t/how-can-i-improve-very-low-assigned-rate-in-featurecounts/758)
**Author:** [@Satsea](https://help.galaxyproject.org/u/Satsea)\ **Replies:** 10\ **Last updated:** [March 11, 2019, 6:15pm UTC](https://help.galaxyproject.org/t/how-can-i-improve-very-low-assigned-rate-in-featurecounts/758 "2019-03-11T18:15:55Z")
I"m a new to Galaxy. I’m trying to analyze my RNA seq data from mice using HISAT2 (or STAR) and featureCount. My data are stranded paired end. I could get a good mapping rate in HISAT2, but only 30% of reads were assi… --- ## [Jobs running for 4+ days with no progress](https://help.galaxyproject.org/t/jobs-running-for-4-days-with-no-progress/18027)
**Author:** [@AEJ](https://help.galaxyproject.org/u/AEJ)\ **Replies:** 1\ **Last updated:** [June 10, 2026, 3:24am UTC](https://help.galaxyproject.org/t/jobs-running-for-4-days-with-no-progress/18027 "2026-06-10T03:24:46Z")
I’ve started a job with RNA Star on Friday (June 4) and it successfully completed 5 of my files, but the other ones haven’t had any progress in days (2 are “Running” and the other 3 haven’t begun yet. Is the server just … --- ## [Resistance gene identifier (RGI) version incompatible with latest CARD database](https://help.galaxyproject.org/t/resistance-gene-identifier-rgi-version-incompatible-with-latest-card-database/17749)
**Author:** [@luc](https://help.galaxyproject.org/u/luc)\ **Replies:** 3\ **Last updated:** [May 27, 2026, 7:23pm UTC](https://help.galaxyproject.org/t/resistance-gene-identifier-rgi-version-incompatible-with-latest-card-database/17749 "2026-05-27T19:23:00Z")
I noticed usegalaxy’s version of RGI (5.2.1) is incompatible with the latest CARD database, can someone look into this? --- ## [Action requires account activation - account created using Gmail address so can't reset password](https://help.galaxyproject.org/t/action-requires-account-activation-account-created-using-gmail-address-so-cant-reset-password/17718)
**Author:** [@kmkocot](https://help.galaxyproject.org/u/kmkocot)\ **Replies:** 4\ **Last updated:** [May 13, 2026, 8:08pm UTC](https://help.galaxyproject.org/t/action-requires-account-activation-account-created-using-gmail-address-so-cant-reset-password/17718 "2026-05-13T20:08:05Z")
I created my usegalaxy account using my gmail (kmkocot@gmail.com) address and I keep getting this error when trying to start a job (mitos2 is the tool I’m trying to use). To the best of my knowledge, my account is alread… --- ## [Fastp was disabled before the job completed](https://help.galaxyproject.org/t/fastp-was-disabled-before-the-job-completed/17720)
**Author:** [@TLhelp](https://help.galaxyproject.org/u/TLhelp)\ **Replies:** 1\ **Last updated:** [May 11, 2026, 6:32pm UTC](https://help.galaxyproject.org/t/fastp-was-disabled-before-the-job-completed/17720 "2026-05-11T18:32:42Z")
I uploaded my fastq data and ran QC. The report showed the data was good enough. But when I ran fastp for adaptor trimming, the tool was disabled before the job completed. It kept showing the same error messages after I … --- ## [Fastp 1.3.3+galaxy0 error: How do i contact my administrator? Workaround: Use version 1.3.2+galaxy0 instead!](https://help.galaxyproject.org/t/fastp-1-3-3-galaxy0-error-how-do-i-contact-my-administrator-workaround-use-version-1-3-2-galaxy0-instead/17712)
**Author:** [@Pedro\_Fernandes\_de\_S](https://help.galaxyproject.org/u/Pedro_Fernandes_de_S)\ **Replies:** 2\ **Last updated:** [May 8, 2026, 11:31pm UTC](https://help.galaxyproject.org/t/fastp-1-3-3-galaxy0-error-how-do-i-contact-my-administrator-workaround-use-version-1-3-2-galaxy0-instead/17712 "2026-05-08T23:31:22Z")
I was trying to use fastp but every time i ran it, it came back with an error that says “This tool was disabled before the job completed. Please contact your Galaxy administrator” --- ## [Is it possible to get the BOLDistilled COI available as a database for Kraken2?](https://help.galaxyproject.org/t/is-it-possible-to-get-the-boldistilled-coi-available-as-a-database-for-kraken2/17696)
**Author:** [@prof.garrison.smc](https://help.galaxyproject.org/u/prof.garrison.smc)\ **Replies:** 8\ **Last updated:** [May 7, 2026, 10:13pm UTC](https://help.galaxyproject.org/t/is-it-possible-to-get-the-boldistilled-coi-available-as-a-database-for-kraken2/17696 "2026-05-07T22:13:00Z")
Hi, We are starting to use Galaxy to analyze our eDNA data. Since we are using PCR for the COI locus, we can accelerate taxonomic assignment by focusing on the COI sequences in a database like the BOLDistilled datasets.… --- ## [Cut Issue Related to Metagenomic](https://help.galaxyproject.org/t/cut-issue-related-to-metagenomic/17698)
**Author:** [@Arif\_Omar](https://help.galaxyproject.org/u/Arif_Omar)\ **Replies:** 1\ **Last updated:** [April 30, 2026, 10:03pm UTC](https://help.galaxyproject.org/t/cut-issue-related-to-metagenomic/17698 "2026-04-30T22:03:42Z")
Hi, I am trying to use the cut on my “Predicted taxon relative abundance (output of Metaphlan)” but it seems like it has taken more than 30 minutes now. Am i doing anything wrongly here? I have also tried to cut c1,c3 an… --- ## [Hosting to UCSC with Custom Builds](https://help.galaxyproject.org/t/hosting-to-ucsc-with-custom-builds/17676)
**Author:** [@GalaxyFrog](https://help.galaxyproject.org/u/GalaxyFrog)\ **Replies:** 5\ **Last updated:** [April 25, 2026, 4:21pm UTC](https://help.galaxyproject.org/t/hosting-to-ucsc-with-custom-builds/17676 "2026-04-25T16:21:51Z")
I love Galaxy! I’m working with the white-tail deer genome build, which is curated by UCSC in it’s most recent form as Ovbor\_1.2 Oct. 2024 white-tailed deer (Illinois 20LAN1187 2024) (GCF\_023699985.2). As near as I can … --- ## [Action requires account activation](https://help.galaxyproject.org/t/action-requires-account-activation/17679)
**Author:** [@Xinyi](https://help.galaxyproject.org/u/Xinyi)\ **Replies:** 2\ **Last updated:** [April 24, 2026, 9:16pm UTC](https://help.galaxyproject.org/t/action-requires-account-activation/17679 "2026-04-24T21:16:43Z")
Action requires account activation. The server could not complete this request. Please verify your parameter settings, retry submission and contact the Galaxy Team if this error persists. A transcript of the submitted da… --- ## [Stuck in queue SPAdes](https://help.galaxyproject.org/t/stuck-in-queue-spades/17684)
**Author:** [@yannick.fornoville](https://help.galaxyproject.org/u/yannick.fornoville)\ **Replies:** 1\ **Last updated:** [April 24, 2026, 7:12pm UTC](https://help.galaxyproject.org/t/stuck-in-queue-spades/17684 "2026-04-24T19:12:57Z")
Hello, im working on a Whole Genome Sequencing of my bacteria but i’m stuck with SPAdes. I’m stuck in queue since yesterday. Is there anything i could do to improve the workflow? Thank you Yannick --- ## [Hyperparameter search missing option](https://help.galaxyproject.org/t/hyperparameter-search-missing-option/17682)
**Author:** [@dillman](https://help.galaxyproject.org/u/dillman)\ **Replies:** 3\ **Last updated:** [April 24, 2026, 6:48pm UTC](https://help.galaxyproject.org/t/hyperparameter-search-missing-option/17682 "2026-04-24T18:48:39Z")
Hello all, I am trying to run the Age prediction using machine learning tutorial and in the Analyze RNA seq data section under optimize hyperparameters in the Hands On: Hyperparameter search it says to set param-repeat “… --- ## [Request Adding Salmonella cgMLST (3002 loci) scheme for CoreProfiler allele\_calling](https://help.galaxyproject.org/t/request-adding-salmonella-cgmlst-3002-loci-scheme-for-coreprofiler-allele-calling/17669)
**Author:** [@Sudipta\_Talukder](https://help.galaxyproject.org/u/Sudipta_Talukder)\ **Replies:** 1\ **Last updated:** [April 22, 2026, 5:33pm UTC](https://help.galaxyproject.org/t/request-adding-salmonella-cgmlst-3002-loci-scheme-for-coreprofiler-allele-calling/17669 "2026-04-22T17:33:11Z")
How to install the EnteroBase Salmonella enterica cgMLST (3002 loci) scheme for CoreProfiler allele\_calling tool on galaxy? --- ## [Issue at RNA-STAR step: adjusting GTF annotation](https://help.galaxyproject.org/t/issue-at-rna-star-step-adjusting-gtf-annotation/17668)
**Author:** [@Sanjukta\_Ghosh](https://help.galaxyproject.org/u/Sanjukta_Ghosh)\ **Replies:** 3\ **Last updated:** [April 22, 2026, 4:56pm UTC](https://help.galaxyproject.org/t/issue-at-rna-star-step-adjusting-gtf-annotation/17668 "2026-04-22T16:56:34Z")
Hello Team, I am performing Refernce based RNA-Seq analysis, and I am stuck at the RNA STAR-based mapping step. After running with the following parameters, an error shows: An error occurred with this dataset. I am not … --- ## [Error while running metaspades](https://help.galaxyproject.org/t/error-while-running-metaspades/9796)
**Author:** [@chi1989](https://help.galaxyproject.org/u/chi1989)\ **Replies:** 2\ **Last updated:** [April 18, 2026, 2:35am UTC](https://help.galaxyproject.org/t/error-while-running-metaspades/9796 "2026-04-18T02:35:14Z")
Hi all, I am running Metaspade on my genome data. I have got { “code\_desc”: “”, “desc”: “Fatal error: Exit code 120 ()”, “error\_level”: 3, “exit\_code”: 120, “type”: “exit\_code” } as my error message. What has gone wron… --- ## [Error with de novo assembly using Trintiy](https://help.galaxyproject.org/t/error-with-de-novo-assembly-using-trintiy/10563)
**Author:** [@Jose\_Manuel\_Latorre](https://help.galaxyproject.org/u/Jose_Manuel_Latorre)\ **Replies:** 5\ **Last updated:** [April 18, 2026, 2:28am UTC](https://help.galaxyproject.org/t/error-with-de-novo-assembly-using-trintiy/10563 "2026-04-18T02:28:46Z")
Dear Galaxy users, First, thanks in advance for your help, I am trying to get a de novo assembly from RNA-Seq data using Trintiy. I have just one sample that was sequenced in the Illumina platform with more or less 40 … --- ## [Help with extracting genome sequences from MAF data](https://help.galaxyproject.org/t/help-with-extracting-genome-sequences-from-maf-data/695)
**Author:** [@la466](https://help.galaxyproject.org/u/la466)\ **Replies:** 3\ **Last updated:** [April 18, 2026, 12:33am UTC](https://help.galaxyproject.org/t/help-with-extracting-genome-sequences-from-maf-data/695 "2026-04-18T00:33:37Z")
Hi I wish to extract alignments between sequences for human and macaque, for which I have the genome coordinates of the human (hg19) in bed format. If I upload a file containing the entry below: chr1 840486 841186 XLOC… --- ## [Extract pairwise maf blocks tools asks for maf source but says 'no options available'](https://help.galaxyproject.org/t/extract-pairwise-maf-blocks-tools-asks-for-maf-source-but-says-no-options-available/10231)
**Author:** [@Deuterium09](https://help.galaxyproject.org/u/Deuterium09)\ **Replies:** 5\ **Last updated:** [April 18, 2026, 12:31am UTC](https://help.galaxyproject.org/t/extract-pairwise-maf-blocks-tools-asks-for-maf-source-but-says-no-options-available/10231 "2026-04-18T00:31:52Z")
I am sending data from UCSC table browser to galaxy in BED format. The data is exons from a gene from the GRCh37/hg19 database. When entering the input file into extract pairwise maf blocks, the choose maf source paramet… --- ## [Help extracting pairwise alignments from MAFs](https://help.galaxyproject.org/t/help-extracting-pairwise-alignments-from-mafs/5481)
**Author:** [@jamesdgalbraith](https://help.galaxyproject.org/u/jamesdgalbraith)\ **Replies:** 2\ **Last updated:** [April 18, 2026, 12:21am UTC](https://help.galaxyproject.org/t/help-extracting-pairwise-alignments-from-mafs/5481 "2026-04-18T00:21:52Z")
Hi, I’ve been attempting to extract the pairwise alignments from the human and zebrafish genomes using the “Extract Pairwise MAF Blocks” tool but had no success. A few years ago I was able complete this with hg19 and da… --- ## [Convert a large maf file to a fasta file](https://help.galaxyproject.org/t/convert-a-large-maf-file-to-a-fasta-file/6123)
**Author:** [@Zi\_Tao](https://help.galaxyproject.org/u/Zi_Tao)\ **Replies:** 2\ **Last updated:** [April 18, 2026, 12:18am UTC](https://help.galaxyproject.org/t/convert-a-large-maf-file-to-a-fasta-file/6123 "2026-04-18T00:18:46Z")
Hi, I’m trying to transfer a large maf file(446MB) to a fasta file, one sequence per species. I used FTP to upload, and while the tool was working it threw an error, saying it’s running out of the disk. So I’m wondering … --- ## [Issue with join maf by species](https://help.galaxyproject.org/t/issue-with-join-maf-by-species/4198)
**Author:** [@Yuncheng\_Duan](https://help.galaxyproject.org/u/Yuncheng_Duan)\ **Replies:** 4\ **Last updated:** [April 18, 2026, 12:17am UTC](https://help.galaxyproject.org/t/issue-with-join-maf-by-species/4198 "2026-04-18T00:17:39Z")
Hi, I’ve been using the join maf by species tool for a long time, it always works very well. However, it started to report error since today. The massage I got is:“The server could not complete the request. Please conta… --- ## ['Extract Pairwise MAF Blocks' unable to detect .maf file](https://help.galaxyproject.org/t/extract-pairwise-maf-blocks-unable-to-detect-maf-file/16403)
**Author:** [@Maggie\_Hassler](https://help.galaxyproject.org/u/Maggie_Hassler)\ **Replies:** 2\ **Last updated:** [April 18, 2026, 12:16am UTC](https://help.galaxyproject.org/t/extract-pairwise-maf-blocks-unable-to-detect-maf-file/16403 "2026-04-18T00:16:26Z")
Hi all, I saw that several people have had similar issues with this tool but none of the solutions really clarified what the issue is here. I have BED files with genomic regions that I got using the GRCh38 reference seq… --- ## [Trackster error? Try IGV instead!](https://help.galaxyproject.org/t/trackster-error-try-igv-instead/4060)
**Author:** [@enten](https://help.galaxyproject.org/u/enten)\ **Replies:** 1\ **Last updated:** [April 14, 2026, 7:43pm UTC](https://help.galaxyproject.org/t/trackster-error-try-igv-instead/4060 "2026-04-14T19:43:17Z")
Hello, I am using BWA to map a yeast WGS on a custom genome that I uploaded in my history. When I try to visualize the mapping using Trackster and picking the custome genome build for the indexing, I get the following … --- ## [A built-in reference genome is not available for zebrafish to utilise HISAT2](https://help.galaxyproject.org/t/a-built-in-reference-genome-is-not-available-for-zebrafish-to-utilise-hisat2/17651)
**Author:** [@Rahul\_Madaan](https://help.galaxyproject.org/u/Rahul_Madaan)\ **Replies:** 1\ **Last updated:** [April 13, 2026, 7:51pm UTC](https://help.galaxyproject.org/t/a-built-in-reference-genome-is-not-available-for-zebrafish-to-utilise-hisat2/17651 "2026-04-13T19:51:59Z")
How do i move ahead…Is there any built in reference genome available that I can just directly upload onto it (from ENSEMBL ?) --- ## [Error during dada2: mergePairs step in DADA2 16S Tutorial](https://help.galaxyproject.org/t/error-during-dada2-mergepairs-step-in-dada2-16s-tutorial/17634)
**Author:** [@zahir](https://help.galaxyproject.org/u/zahir)\ **Replies:** 2\ **Last updated:** [April 10, 2026, 12:01am UTC](https://help.galaxyproject.org/t/error-during-dada2-mergepairs-step-in-dada2-16s-tutorial/17634 "2026-04-10T00:01:13Z")
Hello I am following the Building an amplicon sequence variant (ASV) table from 16S data using DADA2 I follow all the steps until Infer Sample Composition via dada2:dada but crash into error at the Merge paired reads … --- ## [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… [Previous page](https://help.galaxyproject.org/c/usegalaxy-org-support/5.md) [Next page](https://help.galaxyproject.org/c/usegalaxy-org-support/5.md?page=2)