# \#upload **URL:** https://help.galaxyproject.org/tag/upload/25.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Galaxy upload job stuck in ready state and dataset remains 0 B](https://help.galaxyproject.org/t/galaxy-upload-job-stuck-in-ready-state-and-dataset-remains-0-b/18442)
**Author:** [@15802092671](https://help.galaxyproject.org/u/15802092671)\ **Replies:** 1\ **Last updated:** [October 7, 2026, 12:11am UTC](https://help.galaxyproject.org/t/galaxy-upload-job-stuck-in-ready-state-and-dataset-remains-0-b/18442 "2026-10-07T00:11:16Z")
Hi, I am following the Galaxy Training Network Quality Control tutorial and trying to upload the tutorial file: female\_oral2.fastq-4143.gz The file is very small, about 132 KB. I uploaded it from my local computer, b… --- ## [Failed to betaupload](https://help.galaxyproject.org/t/failed-to-betaupload/18377)
**Author:** [@arbv](https://help.galaxyproject.org/u/arbv)\ **Replies:** 1\ **Last updated:** [September 11, 2026, 8:06pm UTC](https://help.galaxyproject.org/t/failed-to-betaupload/18377 "2026-09-11T20:06:35Z")
Server: usegalaxy.org Upload method: Import Data (Beta) File: MDMS240000022-3a\_L1\_1.fq.gz Size: 6.1 GB Target history: SJ29\_assembly\_mapping\_BWA Upload Progress shows 100% completed, but the dataset does not appear … --- ## [Requesting Activation of FTP](https://help.galaxyproject.org/t/requesting-activation-of-ftp/18379)
**Author:** [@ephillippi](https://help.galaxyproject.org/u/ephillippi)\ **Replies:** 1\ **Last updated:** [September 10, 2026, 6:22pm UTC](https://help.galaxyproject.org/t/requesting-activation-of-ftp/18379 "2026-09-10T18:22:13Z")
I am trying to upload 100-300GB files for analysis. The upload has failed multiple times in the web uploader. I really need to be able to restart an upload when there are network hiccups, but FTP is not an option availab… --- ## [Data Upload delays UseGalaxy.org Sept 2026](https://help.galaxyproject.org/t/data-upload-delays-usegalaxy-org-sept-2026/18375)
**Author:** [@Linda\_Kaira](https://help.galaxyproject.org/u/Linda_Kaira)\ **Replies:** 3\ **Last updated:** [September 10, 2026, 4:45pm UTC](https://help.galaxyproject.org/t/data-upload-delays-usegalaxy-org-sept-2026/18375 "2026-09-10T16:45:50Z")
Good day, I have an issue of my data having queued for over 24 hours and even if I upload new data I am still receiving a queued status. I have even started a new history but it is still giving me a queued status --- ## [Uploading Fastq.gz is very slow](https://help.galaxyproject.org/t/uploading-fastq-gz-is-very-slow/18315)
**Author:** [@Yanzi](https://help.galaxyproject.org/u/Yanzi)\ **Replies:** 3\ **Last updated:** [August 24, 2026, 9:02am UTC](https://help.galaxyproject.org/t/uploading-fastq-gz-is-very-slow/18315 "2026-08-24T09:02:33Z")
Hi, I want to upload some fastq.gz files to eu server, together 180G size. But the uploading speed is very slow, which normally is very fast from my previous experience. I can’t finish upload one file (8Gb) in 2 hours. I… --- ## [Repeated DATA\_FETCH failures affecting multiple FASTQ datasets](https://help.galaxyproject.org/t/repeated-data-fetch-failures-affecting-multiple-fastq-datasets/18302)
**Author:** [@rega](https://help.galaxyproject.org/u/rega)\ **Replies:** 1\ **Last updated:** [August 19, 2026, 7:47pm UTC](https://help.galaxyproject.org/t/repeated-data-fetch-failures-affecting-multiple-fastq-datasets/18302 "2026-08-19T19:47:41Z")
Dear Galaxy Support Team, I am experiencing repeated failures when uploading several datasets to Microbiology Galaxy (https://microbiology.usegalaxy.eu/). The problem first occurred with 36\_S36\_R1\_001.fastq.gz, which h… --- ## [Jobs waiting to run](https://help.galaxyproject.org/t/jobs-waiting-to-run/9623)
**Author:** [@christkr08](https://help.galaxyproject.org/u/christkr08)\ **Replies:** 8\ **Last updated:** [June 4, 2023, 2:22pm UTC](https://help.galaxyproject.org/t/jobs-waiting-to-run/9623 "2023-06-04T14:22:51Z")
Hi all, I have uploaded my WGS fq.gz files yesterday but they are still waiting to run… Anyone else with similar problems or with any suggestion? Thanks for any help. --- ## [I don’t have the option to transfer files from an FTP server to my history on Galaxy.org](https://help.galaxyproject.org/t/i-don-t-have-the-option-to-transfer-files-from-an-ftp-server-to-my-history-on-galaxy-org/18176)
**Author:** [@Robert\_Rekawiecki](https://help.galaxyproject.org/u/Robert_Rekawiecki)\ **Replies:** 4\ **Last updated:** [July 21, 2026, 7:17am UTC](https://help.galaxyproject.org/t/i-don-t-have-the-option-to-transfer-files-from-an-ftp-server-to-my-history-on-galaxy-org/18176 "2026-07-21T07:17:11Z")
I don’t have the option to transfer files from an FTP server to my history on Galaxy.org. Unfortunately, Paste/Fetch Data isn’t working either and is displaying an error. I’m trying to transfer files directly from my com… --- ## [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 --- ## [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… --- ## [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… --- ## [Issue : file export with data convert (waters connect)](https://help.galaxyproject.org/t/issue-file-export-with-data-convert-waters-connect/17639)
**Author:** [@Aurelie](https://help.galaxyproject.org/u/Aurelie)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 5:31pm UTC](https://help.galaxyproject.org/t/issue-file-export-with-data-convert-waters-connect/17639 "2026-04-08T17:31:50Z")
In MSnbase readMSData, when I use file mzmL export from data convert (waters connect) : issue occur with this message : Can you tell me why please? --- ## [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? --- ## [GSE accession upload creates grey datasets with 0 pairs on usegalaxy.org](https://help.galaxyproject.org/t/gse-accession-upload-creates-grey-datasets-with-0-pairs-on-usegalaxy-org/17458)
**Author:** [@prabalraj](https://help.galaxyproject.org/u/prabalraj)\ **Replies:** 1\ **Last updated:** [February 16, 2026, 4:33pm UTC](https://help.galaxyproject.org/t/gse-accession-upload-creates-grey-datasets-with-0-pairs-on-usegalaxy-org/17458 "2026-02-16T16:33:58Z")
I am using usegalaxy.org and tried to import data using a GSE accession with the SRA/ENA download tool. The job completed, and I received: One paired-end dataset (green) with 6 fastqsanger.gz pairs One single-end … --- ## [“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… --- ## [Protected data and public UseGalaxy servers](https://help.galaxyproject.org/t/protected-data-and-public-usegalaxy-servers/17426)
**Author:** [@kabrooks2](https://help.galaxyproject.org/u/kabrooks2)\ **Replies:** 2\ **Last updated:** [February 8, 2026, 9:26pm UTC](https://help.galaxyproject.org/t/protected-data-and-public-usegalaxy-servers/17426 "2026-02-08T21:26:19Z")
Hi, I’m new to Galaxy and registered using a protocol provided by my professor. The registration was successful, but when I attempted to retrieve my data using “Faster Download and Extract Reads in FASTQ format from NCB… --- ## [Fastq files not uploading](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484)
**Author:** [@imperialadmiral121](https://help.galaxyproject.org/u/imperialadmiral121)\ **Replies:** 20\ **Last updated:** [February 3, 2026, 4:10pm UTC](https://help.galaxyproject.org/t/fastq-files-not-uploading/16484 "2026-02-03T16:10:09Z")
Fastq files have not uploaded for the past couple of hours, but no outage indicated on the status page. --- ## [Why .nwk file showed as .txt file in galaxy](https://help.galaxyproject.org/t/why-nwk-file-showed-as-txt-file-in-galaxy/16568)
**Author:** [@jinglin](https://help.galaxyproject.org/u/jinglin)\ **Replies:** 2\ **Last updated:** [December 12, 2025, 6:14pm UTC](https://help.galaxyproject.org/t/why-nwk-file-showed-as-txt-file-in-galaxy/16568 "2025-12-12T18:14:10Z")
Hi all, I’m trying to use codeML PAML package in glaaxy, it need newick tree. I made the maxium likelihood tree in MEGA and export as .nwk file. The galaxy tool require .nhx file, so I try to convert .nwk to .nhx via et… --- ## [Download and Extract Reads in FASTQ: Troubleshooting Fatal error: Exit code 2 ()](https://help.galaxyproject.org/t/download-and-extract-reads-in-fastq-troubleshooting-fatal-error-exit-code-2/16482)
**Author:** [@abhi\_g](https://help.galaxyproject.org/u/abhi_g)\ **Replies:** 1\ **Last updated:** [November 10, 2025, 7:30pm UTC](https://help.galaxyproject.org/t/download-and-extract-reads-in-fastq-troubleshooting-fatal-error-exit-code-2/16482 "2025-11-10T19:30:36Z")
I have also faced the sample problem when extracting an sra file using Download and Extract Reads in FASTQ tool. Kindly share your help. --- ## [Upload files stuck in queue](https://help.galaxyproject.org/t/upload-files-stuck-in-queue/16470)
**Author:** [@jperkins](https://help.galaxyproject.org/u/jperkins)\ **Replies:** 3\ **Last updated:** [November 6, 2025, 8:02pm UTC](https://help.galaxyproject.org/t/upload-files-stuck-in-queue/16470 "2025-11-06T20:02:44Z")
I have been unable to upload any files to usegalaxy.org for nearly 24hours. Files will process through the upload-tool and show up in the history but will be stuck in the queue forever. I allowed some to sit overnight to… --- ## [Jobs keep pausing in](https://help.galaxyproject.org/t/jobs-keep-pausing-in/16442)
**Author:** [@andreas\_huysman](https://help.galaxyproject.org/u/andreas_huysman)\ **Replies:** 5\ **Last updated:** [October 29, 2025, 4:34pm UTC](https://help.galaxyproject.org/t/jobs-keep-pausing-in/16442 "2025-10-29T16:34:43Z")
Hi, While I have done some RNA seq analysis, it’s the first time i’m using Galaxy. I’m uploading 15 FastQ.gz files, this took some time but they’re uploaded. Now running the jobs per file is quite the struggle. Six of t… --- ## [Upload tool troubleshooting at UseGalaxy.org](https://help.galaxyproject.org/t/upload-tool-troubleshooting-at-usegalaxy-org/16407)
**Author:** [@khorvat](https://help.galaxyproject.org/u/khorvat)\ **Replies:** 1\ **Last updated:** [October 17, 2025, 7:12pm UTC](https://help.galaxyproject.org/t/upload-tool-troubleshooting-at-usegalaxy-org/16407 "2025-10-17T19:12:34Z")
Now I have that same issue on .org server. It’s stuck forever on 0% for my fastq.gz files --- ## [Using filezilla for uploading large files](https://help.galaxyproject.org/t/using-filezilla-for-uploading-large-files/16266)
**Author:** [@richard64](https://help.galaxyproject.org/u/richard64)\ **Replies:** 20\ **Last updated:** [October 8, 2025, 9:35pm UTC](https://help.galaxyproject.org/t/using-filezilla-for-uploading-large-files/16266 "2025-10-08T21:35:22Z")
I have downloaded filezilla and it is asking for host username password and port. I can sort username and password but what host name and port should I input --- ## [Error in using FastQC in Galaxy EU](https://help.galaxyproject.org/t/error-in-using-fastqc-in-galaxy-eu/16330)
**Author:** [@Pedro\_Fernandes\_de\_S](https://help.galaxyproject.org/u/Pedro_Fernandes_de_S)\ **Replies:** 2\ **Last updated:** [October 2, 2025, 7:40am UTC](https://help.galaxyproject.org/t/error-in-using-fastqc-in-galaxy-eu/16330 "2025-10-02T07:40:17Z")
I have already used fastqc sometimes inGalaxy, but for a specific dataset it is not working, it says something about it being a not GZip archive but i dont even know what isthis, can someone help? --- ## [Tool 'sra\_source' does not exist](https://help.galaxyproject.org/t/tool-sra-source-does-not-exist/16274)
**Author:** [@Atefeh\_Bahmei](https://help.galaxyproject.org/u/Atefeh_Bahmei)\ **Replies:** 2\ **Last updated:** [September 23, 2025, 6:52pm UTC](https://help.galaxyproject.org/t/tool-sra-source-does-not-exist/16274 "2025-09-23T18:52:48Z")
Hi my friends. I have a paired-end data (PRJNA998059) I wanna analyze it with GALAXY. However, when I wanna deliver it from GEO NCBI site to galaxy I get this error “Tool ‘sra\_source’ does not exist.” Is there any soluti… --- ## [Slow uploading of files](https://help.galaxyproject.org/t/slow-uploading-of-files/16261)
**Author:** [@Ines\_Leao](https://help.galaxyproject.org/u/Ines_Leao)\ **Replies:** 1\ **Last updated:** [September 16, 2025, 11:02pm UTC](https://help.galaxyproject.org/t/slow-uploading-of-files/16261 "2025-09-16T23:02:03Z")
Hello everyone! I´ve been trying this morning to upload files containing sequences that I want to cluster using cd-hit. My files are in the format fasta, but they can be considered heavy since their size is 79 622 KB a… --- ## [Uploading files](https://help.galaxyproject.org/t/uploading-files/16255)
**Author:** [@richard64](https://help.galaxyproject.org/u/richard64)\ **Replies:** 1\ **Last updated:** [September 15, 2025, 10:24pm UTC](https://help.galaxyproject.org/t/uploading-files/16255 "2025-09-15T22:24:45Z")
Hello I have 6 files each of 39GB to upload. Can I upload them using the local files tab. (my upload speed is 300mbps) --- ## [Galaxy Collection Upload Not Working](https://help.galaxyproject.org/t/galaxy-collection-upload-not-working/16233)
**Author:** [@Anisha\_Dhanjal](https://help.galaxyproject.org/u/Anisha_Dhanjal)\ **Replies:** 5\ **Last updated:** [September 8, 2025, 5:42pm UTC](https://help.galaxyproject.org/t/galaxy-collection-upload-not-working/16233 "2025-09-08T17:42:20Z")
When uploading files to a collection once all files turn green after pressing start Galaxy won’t let me press build… --- ## [Trouble Uploading Files to Local Galaxy v25 on Shared HPC](https://help.galaxyproject.org/t/trouble-uploading-files-to-local-galaxy-v25-on-shared-hpc/16235)
**Author:** [@hohosharon](https://help.galaxyproject.org/u/hohosharon)\ **Replies:** 2\ **Last updated:** [September 6, 2025, 3:45am UTC](https://help.galaxyproject.org/t/trouble-uploading-files-to-local-galaxy-v25-on-shared-hpc/16235 "2025-09-06T03:45:03Z")
Hi everyone, I recently set up a local Galaxy v25 instance on a VM in a shared HPC environment. However, I am unable to upload any files to this Galaxy instance. When I try to upload a file, the upload tool keeps showi… [Next page](https://help.galaxyproject.org/tag/upload/25.md?match_all_tags=true&page=1&tags%5B%5D=upload)