# \#usinggalaxy **URL:** https://help.galaxyproject.org/tag/usinggalaxy/281.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [ChemFlow – Account Activation Issue](https://help.galaxyproject.org/t/chemflow-account-activation-issue/18624)
**Author:** [@soukaina.maouli](https://help.galaxyproject.org/u/soukaina.maouli)\ **Replies:** 3\ **Last updated:** [November 12, 2026, 7:24pm UTC](https://help.galaxyproject.org/t/chemflow-account-activation-issue/18624 "2026-11-12T19:24:59Z")
Hi, I recently created an account on ChemFlow using my institutional email address (Mines Paris – PSL). I received the account activation email and clicked on the activation link. However, instead of receiving a confirm… --- ## [Storage quota increase request – account theo\_9800 (usegalaxy.fr)](https://help.galaxyproject.org/t/storage-quota-increase-request-account-theo-9800-usegalaxy-fr/18479)
**Author:** [@Theo](https://help.galaxyproject.org/u/Theo)\ **Replies:** 1\ **Last updated:** [October 17, 2026, 12:05am UTC](https://help.galaxyproject.org/t/storage-quota-increase-request-account-theo-9800-usegalaxy-fr/18479 "2026-10-17T00:05:09Z")
Hello, I’m a research engineer at the MetaToul-AXIOM metabolomics platform (INRAE Toxalim, Toulouse). I’m processing a large untargeted LC-MS dataset with XCMS-based tools on, and my current 100 GB quota is no longer en… --- ## [Cannot access the tutorial material to conduct LefSe anaysis on Galaxy](https://help.galaxyproject.org/t/cannot-access-the-tutorial-material-to-conduct-lefse-anaysis-on-galaxy/18454)
**Author:** [@N123](https://help.galaxyproject.org/u/N123)\ **Replies:** 1\ **Last updated:** [October 14, 2026, 6:15pm UTC](https://help.galaxyproject.org/t/cannot-access-the-tutorial-material-to-conduct-lefse-anaysis-on-galaxy/18454 "2026-10-14T18:15:41Z")
Can anyone provide the tutorial materials for conducting LefSe analysis on Galaxy? The tutorial link shows Repository not found. --- ## [Fatal Erreur Exit code 1 sur xcms findChromPeaks (v3.12.0+galaxy4)](https://help.galaxyproject.org/t/fatal-erreur-exit-code-1-sur-xcms-findchrompeaks-v3-12-0-galaxy4/18427)
**Author:** [@Theo](https://help.galaxyproject.org/u/Theo)\ **Replies:** 3\ **Last updated:** [October 1, 2026, 9:58am UTC](https://help.galaxyproject.org/t/fatal-erreur-exit-code-1-sur-xcms-findchrompeaks-v3-12-0-galaxy4/18427 "2026-10-01T09:58:16Z")
Hello, I am writing to report a systematic error when running a job on the Workflow4Metabolomics platform. The xcms findChromPeaks (xcmsSet) tool repeatedly fails during chromatographic peak detection. Job details: … --- ## [UseGalaxy.fr service updates re: IFB Core Cluster infrastructure shutdown from September 14th to 21st, 2026](https://help.galaxyproject.org/t/usegalaxy-fr-service-updates-re-ifb-core-cluster-infrastructure-shutdown-from-september-14th-to-21st-2026/18409)
**Author:** [@tristan.lefebure](https://help.galaxyproject.org/u/tristan.lefebure)\ **Replies:** 1\ **Last updated:** [September 21, 2026, 7:09pm UTC](https://help.galaxyproject.org/t/usegalaxy-fr-service-updates-re-ifb-core-cluster-infrastructure-shutdown-from-september-14th-to-21st-2026/18409 "2026-09-21T19:09:20Z")
Dear all, Is installing FROGS on usegalaxy\_eu still not possible ? usegalaxy\_fr as an electrical issue, and I can’t find an other alternative… and my training session is next week ;( Thanks --- ## [GALAXY/ BRIDGE failure submitting job](https://help.galaxyproject.org/t/galaxy-bridge-failure-submitting-job/18288)
**Author:** [@zineddine](https://help.galaxyproject.org/u/zineddine)\ **Replies:** 1\ **Last updated:** [August 18, 2026, 4:12am UTC](https://help.galaxyproject.org/t/galaxy-bridge-failure-submitting-job/18288 "2026-08-18T04:12:03Z")
I’m having some problems using ‘Gromacs Initial Setup’; the task isn’t being submitted, even when I switch web browsers , and the same message appears when using ‘Get PDB’ – and the same may well apply to all the other … --- ## [Galaxy france log in issue](https://help.galaxyproject.org/t/galaxy-france-log-in-issue/18287)
**Author:** [@abul](https://help.galaxyproject.org/u/abul)\ **Replies:** 1\ **Last updated:** [August 18, 2026, 3:58am UTC](https://help.galaxyproject.org/t/galaxy-france-log-in-issue/18287 "2026-08-18T03:58:49Z")
Subject: Workflow4Metabolomics Galaxy login page stuck on Loading Dear Workflow4Metabolomics team, I have been unable to access the Workflow4Metabolomics Galaxy server for the past two days. When I open the login page,… --- ## [Unable to access Galaxy (Connection timed out)](https://help.galaxyproject.org/t/unable-to-access-galaxy-connection-timed-out/18254)
**Author:** [@noamesh11](https://help.galaxyproject.org/u/noamesh11)\ **Replies:** 1\ **Last updated:** [August 7, 2026, 5:02pm UTC](https://help.galaxyproject.org/t/unable-to-access-galaxy-connection-timed-out/18254 "2026-08-07T17:02:02Z")
Hello, I am unable to access the Galaxy server at https://galaxy.biobakery.org in order to continue my MaAsLin2 analysis. Whenever I try to open the website, I receive the following error: ERR\_CONNECTION\_TIMED\_OUT I … --- ## [DADA2 tool issues in Galaxy France](https://help.galaxyproject.org/t/dada2-tool-issues-in-galaxy-france/17706)
**Author:** [@karenandreac](https://help.galaxyproject.org/u/karenandreac)\ **Replies:** 1\ **Last updated:** [May 6, 2026, 6:27am UTC](https://help.galaxyproject.org/t/dada2-tool-issues-in-galaxy-france/17706 "2026-05-06T06:27:00Z")
Hello! I’m working in Galaxy France, and apparently the platform is having some issues loading the tools. Currently I’m running my data with DADA2 since yesterday, and the “learnError” and “dada” tools have been running… --- ## [Problem with falco tool](https://help.galaxyproject.org/t/problem-with-falco-tool/17655)
**Author:** [@Teresa](https://help.galaxyproject.org/u/Teresa)\ **Replies:** 2\ **Last updated:** [April 20, 2026, 5:19pm UTC](https://help.galaxyproject.org/t/problem-with-falco-tool/17655 "2026-04-20T17:19:36Z")
Hi! I’m working on a university assignment and I’m first practicing in Galaxy using an NCBI dataset (SRR17898727). I downloaded it using the tool “faster download and extract reads in FASTQ”. Now I want to apply Falco t… --- ## [SAINTexpress data](https://help.galaxyproject.org/t/saintexpress-data/16394)
**Author:** [@Bernard](https://help.galaxyproject.org/u/Bernard)\ **Replies:** 7\ **Last updated:** [April 8, 2026, 2:22am UTC](https://help.galaxyproject.org/t/saintexpress-data/16394 "2026-04-08T02:22:26Z")
How does one specify if input data submitted to SAINTexpress are spectral counts or MS1 intensities? Also, should MS1 intensities be Log transformed? Thank you --- ## [Problem when deleting data](https://help.galaxyproject.org/t/problem-when-deleting-data/17609)
**Author:** [@Delia\_D](https://help.galaxyproject.org/u/Delia_D)\ **Replies:** 1\ **Last updated:** [March 27, 2026, 2:46pm UTC](https://help.galaxyproject.org/t/problem-when-deleting-data/17609 "2026-03-27T14:46:09Z")
Hello, I am performing RNA-seq analyses on Galaxy. I am working with a 250 GB storage quota, but I do not have enough space to complete all the steps I need (Cutadapt, RNA STAR, etc.). I would like to delete my raw da… --- ## [Issue related to collection created in galaxy](https://help.galaxyproject.org/t/issue-related-to-collection-created-in-galaxy/17615)
**Author:** [@Abhisek\_Dey](https://help.galaxyproject.org/u/Abhisek_Dey)\ **Replies:** 3\ **Last updated:** [March 27, 2026, 10:25am UTC](https://help.galaxyproject.org/t/issue-related-to-collection-created-in-galaxy/17615 "2026-03-27T10:25:29Z")
I used the option to unhide the objects in Galaxy, and all files are showing in individual form. I can’t understand how I can show it in the previous form as a collection. Initially my files were in a collection form. --- ## [Zip file upload paused](https://help.galaxyproject.org/t/zip-file-upload-paused/17532)
**Author:** [@duanyf](https://help.galaxyproject.org/u/duanyf)\ **Replies:** 3\ **Last updated:** [March 4, 2026, 6:45pm UTC](https://help.galaxyproject.org/t/zip-file-upload-paused/17532 "2026-03-04T18:45:40Z")
Not sure why — when uploading a 150 MB file, it turned orange halfway and showed “Warning: Waiting for server to resume…”. Will this resume, or does it mean the upload has failed? --- ## [Using GeMoMa in Galaxy: Genome Annotation in Galaxy](https://help.galaxyproject.org/t/using-gemoma-in-galaxy-genome-annotation-in-galaxy/17477)
**Author:** [@katerinagarkova](https://help.galaxyproject.org/u/katerinagarkova)\ **Replies:** 3\ **Last updated:** [March 2, 2026, 12:26pm UTC](https://help.galaxyproject.org/t/using-gemoma-in-galaxy-genome-annotation-in-galaxy/17477 "2026-03-02T12:26:05Z")
On the GeMoMa website (I am unable to link it, but it’s the Jstacks one) it says that GeMoMa is able to be used within Galaxy, but when searching for it in Galaxy’s tools, I can not find it. Additionally, when I click th… --- ## [ChIP sequencing](https://help.galaxyproject.org/t/chip-sequencing/17461)
**Author:** [@Krishnendu\_Goswami](https://help.galaxyproject.org/u/Krishnendu_Goswami)\ **Replies:** 1\ **Last updated:** [February 16, 2026, 6:02pm UTC](https://help.galaxyproject.org/t/chip-sequencing/17461 "2026-02-16T18:02:34Z")
I am trying to analysis ChIP seq data . I got MultiQC, coverage from MACS2 (bigwig), bedtools annotatedbed on data. I hope i got everything, now i need to go for further step to find the the promoter region, but I am una… --- ## [Galaxy SynBio CAD errors with RetroPath2.0 and RP2pathways](https://help.galaxyproject.org/t/galaxy-synbio-cad-errors-with-retropath2-0-and-rp2pathways/17439)
**Author:** [@Swati\_Kundu](https://help.galaxyproject.org/u/Swati_Kundu)\ **Replies:** 3\ **Last updated:** [February 12, 2026, 5:43pm UTC](https://help.galaxyproject.org/t/galaxy-synbio-cad-errors-with-retropath2-0-and-rp2pathways/17439 "2026-02-12T17:43:30Z")
so I was using Galaxy SynBio CAD, for retrosynthesis, and i used RetroPath2.0 for it, now RetroPath2.0 is supposed to also provide us with a scope matrix, along with the csv, without that csv, i cannot visualize the path… --- ## [“Input Data Is Missing” Error When Retrieving Dataset](https://help.galaxyproject.org/t/input-data-is-missing-error-when-retrieving-dataset/17442)
**Author:** [@kabrooks2](https://help.galaxyproject.org/u/kabrooks2)\ **Replies:** 3\ **Last updated:** [February 12, 2026, 5:41pm UTC](https://help.galaxyproject.org/t/input-data-is-missing-error-when-retrieving-dataset/17442 "2026-02-12T17:41:37Z")
Hello, I’m trying to get data SRR7757114 from Faster Download and Extract Reads in FASTQ format from NCBI SRA, but I have run into an error that says “err: the input data is missing the QUALITY-column”. I’m not sure wha… --- ## [Fasterq-dump and fastq-dump failing on usegalaxy.eu with connection validation error (sra-download-internal)](https://help.galaxyproject.org/t/fasterq-dump-and-fastq-dump-failing-on-usegalaxy-eu-with-connection-validation-error-sra-download-internal/17449)
**Author:** [@OzGuo](https://help.galaxyproject.org/u/OzGuo)\ **Replies:** 3\ **Last updated:** [February 12, 2026, 5:41pm UTC](https://help.galaxyproject.org/t/fasterq-dump-and-fastq-dump-failing-on-usegalaxy-eu-with-connection-validation-error-sra-download-internal/17449 "2026-02-12T17:41:02Z")
Hello, I am experiencing repeated failures when trying to download SRA accessions on usegalaxy.eu using both fastq-dump and fasterq-dump. Example accession: SRR2033948 The job repeatedly fails with the following err… --- ## [RepeatExplorer FTP upload issue](https://help.galaxyproject.org/t/repeatexplorer-ftp-upload-issue/17414)
**Author:** [@karol.krak](https://help.galaxyproject.org/u/karol.krak)\ **Replies:** 4\ **Last updated:** [February 5, 2026, 8:25pm UTC](https://help.galaxyproject.org/t/repeatexplorer-ftp-upload-issue/17414 "2026-02-05T20:25:21Z")
Hi, I was trying to upload data to my RepeatExplorer on galaxy and I run in this error message: directory (/mnt/galaxy-re/uploads/karol\_krak@repeatexplorer-elixir.cerit-sc.cz/) is a symlink to a location not on the all… --- ## [Error in Batch correction step in workflow4metabolomics](https://help.galaxyproject.org/t/error-in-batch-correction-step-in-workflow4metabolomics/17371)
**Author:** [@Abhisek\_Dey](https://help.galaxyproject.org/u/Abhisek_Dey)\ **Replies:** 6\ **Last updated:** [January 29, 2026, 10:56pm UTC](https://help.galaxyproject.org/t/error-in-batch-correction-step-in-workflow4metabolomics/17371 "2026-01-29T22:56:59Z")
I am analyzing metabolomics data with workflow4metabolomics pipeline . I have only normal samples no QC, Pool, and blank samples in our experiment. I want to do batch correction but getting following error when I perform… --- ## [Does SAINTexpress-spc actually use the protein length values from the .Prey file?](https://help.galaxyproject.org/t/does-saintexpress-spc-actually-use-the-protein-length-values-from-the-prey-file/17282)
**Author:** [@Samantha\_Cassity](https://help.galaxyproject.org/u/Samantha_Cassity)\ **Replies:** 1\ **Last updated:** [January 24, 2026, 12:08am UTC](https://help.galaxyproject.org/t/does-saintexpress-spc-actually-use-the-protein-length-values-from-the-prey-file/17282 "2026-01-24T00:08:29Z")
I suspected SAINTexpress-spc was not using protein lengths for anything useful. I ran SAINTexpress-spc with a .Prey file that contains UniprotIDs mapped to their correct protein lengths. I also ran it with a .Prey file t… --- ## [GrowthPred troubleshooting](https://help.galaxyproject.org/t/growthpred-troubleshooting/16559)
**Author:** [@Darshan\_Singh](https://help.galaxyproject.org/u/Darshan_Singh)\ **Replies:** 3\ **Last updated:** [December 15, 2025, 7:12pm UTC](https://help.galaxyproject.org/t/growthpred-troubleshooting/16559 "2025-12-15T19:12:13Z")
Hi, were you able to solve this using the aforementioned solution. When I had done so it did not work. --- ## [Issues running GrowthPred with genomes](https://help.galaxyproject.org/t/issues-running-growthpred-with-genomes/8268)
**Author:** [@Rosave](https://help.galaxyproject.org/u/Rosave)\ **Replies:** 3\ **Last updated:** [September 23, 2022, 6:46pm UTC](https://help.galaxyproject.org/t/issues-running-growthpred-with-genomes/8268 "2022-09-23T18:46:46Z")
Hi I have high-quality draft genomes and I’m having issues running them on GrowthPred to calculate predicted ideal growth temperature. I’ve uploaded the following files (see below) and in all instances I’ve received the… --- ## [iCAMP builds phylogenetic tree based on bin](https://help.galaxyproject.org/t/icamp-builds-phylogenetic-tree-based-on-bin/11366)
**Author:** [@alex\_123](https://help.galaxyproject.org/u/alex_123)\ **Replies:** 5\ **Last updated:** [November 17, 2025, 7:34pm UTC](https://help.galaxyproject.org/t/icamp-builds-phylogenetic-tree-based-on-bin/11366 "2025-11-17T19:34:29Z")
hello! When I use the iCAMP process, I want to build a phylogenetic tree based on bin, but I have searched all over the iCAMP function and there is still no such function. How should I try it? --- ## [Which "galaxy server" is it best to use from Northern China?](https://help.galaxyproject.org/t/which-galaxy-server-is-it-best-to-use-from-northern-china/16497)
**Author:** [@drvjh62](https://help.galaxyproject.org/u/drvjh62)\ **Replies:** 2\ **Last updated:** [November 17, 2025, 10:16am UTC](https://help.galaxyproject.org/t/which-galaxy-server-is-it-best-to-use-from-northern-china/16497 "2025-11-17T10:16:16Z")
Has anyone had any experience with which “galaxy server” is it best to use from Northern China specifically Shenyang?? --- ## [Spider plot error](https://help.galaxyproject.org/t/spider-plot-error/16478)
**Author:** [@ksilence](https://help.galaxyproject.org/u/ksilence)\ **Replies:** 4\ **Last updated:** [November 12, 2025, 1:41am UTC](https://help.galaxyproject.org/t/spider-plot-error/16478 "2025-11-12T01:41:11Z")
Project name;akaxkpad Traceback (most recent call last): File “/protologger2/galaxy/tools/spider\_plot/Spider\_code-v0.1.py”, line 72, in process = subprocess.Popen(bashCommand.split(), stdout=subprocess.PIPE) File "/… --- ## [Can\`t find the tool "protologger"](https://help.galaxyproject.org/t/can-t-find-the-tool-protologger/16370)
**Author:** [@ksilence](https://help.galaxyproject.org/u/ksilence)\ **Replies:** 7\ **Last updated:** [November 1, 2025, 2:20am UTC](https://help.galaxyproject.org/t/can-t-find-the-tool-protologger/16370 "2025-11-01T02:20:01Z")
Last month, I used the tool “protologger“ to analyze my data, but several days ago, I found I couldn\`t search for this tool. How should I use this tool? Are there any alternative methods? I will be very appreciative of y… --- ## [Is W4M under maintenance?](https://help.galaxyproject.org/t/is-w4m-under-maintenance/16448)
**Author:** [@robin\_cahuzac](https://help.galaxyproject.org/u/robin_cahuzac)\ **Replies:** 1\ **Last updated:** [October 29, 2025, 4:50pm UTC](https://help.galaxyproject.org/t/is-w4m-under-maintenance/16448 "2025-10-29T16:50:40Z")
Hello, I can’t get a step to run on W4M. Is the site under maintenance? --- ## [Inclusion of lefse tool for tabular inputs](https://help.galaxyproject.org/t/inclusion-of-lefse-tool-for-tabular-inputs/16351)
**Author:** [@Rachita\_Maruti\_G](https://help.galaxyproject.org/u/Rachita_Maruti_G)\ **Replies:** 1\ **Last updated:** [October 8, 2025, 11:55pm UTC](https://help.galaxyproject.org/t/inclusion-of-lefse-tool-for-tabular-inputs/16351 "2025-10-08T23:55:48Z")
Hi, Right now, Lefse tool in Eu server has the .mothur input format (I have my input in tabular format). Would it possible to add Lefse tool for tabular inputs as it is in biobakery galaxy website which is currently un… [Next page](https://help.galaxyproject.org/tag/usinggalaxy/281.md?match_all_tags=true&page=1&tags%5B%5D=usinggalaxy)