# usegalaxy.eu support **URL:** https://help.galaxyproject.org/c/usegalaxy-eu-support/6.md?page=4 [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) **Page:** 5 --- ## [Trimmomatic error when running SRA data](https://help.galaxyproject.org/t/trimmomatic-error-when-running-sra-data/17594)
**Author:** [@abhi\_g](https://help.galaxyproject.org/u/abhi_g)\ **Replies:** 1\ **Last updated:** [March 20, 2026, 4:34pm UTC](https://help.galaxyproject.org/t/trimmomatic-error-when-running-sra-data/17594 "2026-03-20T16:34:35Z")
Dataset Information Number 12 Name SRR11532725:reverse Created Wednesday Mar 18th 14:25:37 2026 GMT+5:30 Filesize 6.4 MB Dbkey ? Format fastqsanger.gz File contents contents Tool Parameters Inp… --- ## [Ouput unaligned reads into bam file with hisat2](https://help.galaxyproject.org/t/ouput-unaligned-reads-into-bam-file-with-hisat2/17587)
**Author:** [@alixlem](https://help.galaxyproject.org/u/alixlem)\ **Replies:** 1\ **Last updated:** [March 18, 2026, 2:24pm UTC](https://help.galaxyproject.org/t/ouput-unaligned-reads-into-bam-file-with-hisat2/17587 "2026-03-18T14:24:49Z")
Hello, I have a list of genes and a list of RNAs. For each gene, I would like to know how many RNAs do not align. I am using hisat2 for alignments, and it gives me a fastaqsanger file with the unaligned reads, but the b… --- ## [Error in SnpSift tool due to token ANN interpretation and out of memory](https://help.galaxyproject.org/t/error-in-snpsift-tool-due-to-token-ann-interpretation-and-out-of-memory/17573)
**Author:** [@abhi\_g](https://help.galaxyproject.org/u/abhi_g)\ **Replies:** 3\ **Last updated:** [March 18, 2026, 10:06am UTC](https://help.galaxyproject.org/t/error-in-snpsift-tool-due-to-token-ann-interpretation-and-out-of-memory/17573 "2026-03-18T10:06:40Z")
Can the below problem be solved? Kindly suggest. " What the error means Part of the message What it usually means in plain English line 2:8 no viable alternative at input 'ANN' The filter expression you gave to… --- ## [You are not allowed to access this dataset](https://help.galaxyproject.org/t/you-are-not-allowed-to-access-this-dataset/17585)
**Author:** [@NamVo](https://help.galaxyproject.org/u/NamVo)\ **Replies:** 1\ **Last updated:** [March 18, 2026, 8:49am UTC](https://help.galaxyproject.org/t/you-are-not-allowed-to-access-this-dataset/17585 "2026-03-18T08:49:19Z")
When I shared my history, which have raw data and result dataset from tools, to my friend, he can access the raw data but the result dataset. It said “you are not allowed to access this dataset”. The advice is “check a … --- ## [Error while running Humann](https://help.galaxyproject.org/t/error-while-running-humann/17575)
**Author:** [@Ben7124](https://help.galaxyproject.org/u/Ben7124)\ **Replies:** 5\ **Last updated:** [March 18, 2026, 8:35am UTC](https://help.galaxyproject.org/t/error-while-running-humann/17575 "2026-03-18T08:35:02Z")
Hello, I am getting this error when running Humann. Thanks for any help! FATAL: While checking container encryption: could not open image /cvmfs/singularity.galaxyproject.org/all/humann:3.9--py312hdfd78af\_0: failed t… --- ## [Galaxy EU Server: Downtime March 16, 17 2026](https://help.galaxyproject.org/t/galaxy-eu-server-downtime-march-16-17-2026/17580)
**Author:** [@kabrooks2](https://help.galaxyproject.org/u/kabrooks2)\ **Replies:** 2\ **Last updated:** [March 18, 2026, 8:09am UTC](https://help.galaxyproject.org/t/galaxy-eu-server-downtime-march-16-17-2026/17580 "2026-03-18T08:09:55Z")
Hi, while working on my data, I noticed Galaxy stopped responding, so I refreshed the page. When it reloaded, I immediately received the error shown in the picture below. Is the server currently down for everyone else? … --- ## [Missing genes in eggNOG-mapper output: How to explore results across processing steps](https://help.galaxyproject.org/t/missing-genes-in-eggnog-mapper-output-how-to-explore-results-across-processing-steps/17500)
**Author:** [@temobarak](https://help.galaxyproject.org/u/temobarak)\ **Replies:** 3\ **Last updated:** [March 16, 2026, 5:48pm UTC](https://help.galaxyproject.org/t/missing-genes-in-eggnog-mapper-output-how-to-explore-results-across-processing-steps/17500 "2026-03-16T17:48:35Z")
Hello, I am encountering an issue while running eggNOG-mapper on Galaxy. Some protein-coding genes present in my input FASTA file (protein sequences) are missing from the final annotation output file. I have checked ca… --- ## [Cluster on intervals error](https://help.galaxyproject.org/t/cluster-on-intervals-error/17562)
**Author:** [@jmuser](https://help.galaxyproject.org/u/jmuser)\ **Replies:** 5\ **Last updated:** [March 16, 2026, 10:57am UTC](https://help.galaxyproject.org/t/cluster-on-intervals-error/17562 "2026-03-16T10:57:39Z")
I am trying to run Cluster the intervals of a dataset. The dataset was uploaded as a tab-delimited txt file with intervals (chr, start, end), with format set to interval. However, I keep getting an error, for instance. U… --- ## [Error in SnpEff version](https://help.galaxyproject.org/t/error-in-snpeff-version/17563)
**Author:** [@abhi\_g](https://help.galaxyproject.org/u/abhi_g)\ **Replies:** 4\ **Last updated:** [March 14, 2026, 3:39pm UTC](https://help.galaxyproject.org/t/error-in-snpeff-version/17563 "2026-03-14T15:39:06Z")
I used Snpeff on the output of VCFfilter tool at the version 5.2+galaxy1 and the result showed an error. The AI error analysis displayed that it may be due to the database file format changed between the 4.x and 5.x fa… --- ## [GOEnrichment support](https://help.galaxyproject.org/t/goenrichment-support/17568)
**Author:** [@Edith\_Tittarelli](https://help.galaxyproject.org/u/Edith_Tittarelli)\ **Replies:** 1\ **Last updated:** [March 13, 2026, 6:14pm UTC](https://help.galaxyproject.org/t/goenrichment-support/17568 "2026-03-13T18:14:41Z")
Hello, I am currently working with a NON model species in Galaxy (usegalaxy.eu) and I would like to perform GO enrichment analysis. However, I am having trouble understanding how to generate the Gene Product Annotation … --- ## [MITOS2 missing reference data](https://help.galaxyproject.org/t/mitos2-missing-reference-data/17567)
**Author:** [@abbyevewilliams](https://help.galaxyproject.org/u/abbyevewilliams)\ **Replies:** 1\ **Last updated:** [March 13, 2026, 5:53pm UTC](https://help.galaxyproject.org/t/mitos2-missing-reference-data/17567 "2026-03-13T17:53:28Z")
Hi there, I’m annotating some mitochondrial genomes using the MITOS2 webserver but my reference data appears to be missing. I need the Caloenas nicobarica genome (bCalNic1.hap1). I’m not sure how to get in contact with … --- ## [Bowtie2 mapping output](https://help.galaxyproject.org/t/bowtie2-mapping-output/17555)
**Author:** [@Alison](https://help.galaxyproject.org/u/Alison)\ **Replies:** 4\ **Last updated:** [March 12, 2026, 8:08am UTC](https://help.galaxyproject.org/t/bowtie2-mapping-output/17555 "2026-03-12T08:08:55Z")
I’m a new user using Galaxy Europe. I am working through the tutorials then applying my learning to my own data. I have run bowtie 2 on my filtered by quality file (single end reads) but puzzled by the output. I don’t u… --- ## [Bug error from metabolomics workflows](https://help.galaxyproject.org/t/bug-error-from-metabolomics-workflows/17557)
**Author:** [@corlandi147](https://help.galaxyproject.org/u/corlandi147)\ **Replies:** 1\ **Last updated:** [March 11, 2026, 6:12pm UTC](https://help.galaxyproject.org/t/bug-error-from-metabolomics-workflows/17557 "2026-03-11T18:12:32Z")
Hi, I just load my processing workflow for metabolomics data and whatever the story, the grouping step (XCMSgroupChromPeaks) blocks with a bug message error: “ unable to finish job” or “Job output not returned from clu… --- ## [Question about interproscan](https://help.galaxyproject.org/t/question-about-interproscan/17538)
**Author:** [@Mark\_C](https://help.galaxyproject.org/u/Mark_C)\ **Replies:** 9\ **Last updated:** [March 10, 2026, 7:33pm UTC](https://help.galaxyproject.org/t/question-about-interproscan/17538 "2026-03-10T19:33:57Z")
Hello, I am having difficulties with interproscan. I am entering the output from Getorf (fasta) and get the error below. I have tried editing the input to simplify headers, alter line width etc but with no success. Ple… --- ## [Adding Custom PTM Modification in Maxquant Galaxy Tool Configuration](https://help.galaxyproject.org/t/adding-custom-ptm-modification-in-maxquant-galaxy-tool-configuration/17551)
**Author:** [@Rajesh\_saravanan](https://help.galaxyproject.org/u/Rajesh_saravanan)\ **Replies:** 2\ **Last updated:** [March 10, 2026, 11:05am UTC](https://help.galaxyproject.org/t/adding-custom-ptm-modification-in-maxquant-galaxy-tool-configuration/17551 "2026-03-10T11:05:03Z")
Hello everyone, Is it possible to add a custom PTM modification? I would like to know if there is a way to define and include a user-specified PTM apart from the default modification list. --- ## [Bad lineage by Nextclade](https://help.galaxyproject.org/t/bad-lineage-by-nextclade/17544)
**Author:** [@sma](https://help.galaxyproject.org/u/sma)\ **Replies:** 2\ **Last updated:** [March 6, 2026, 7:36am UTC](https://help.galaxyproject.org/t/bad-lineage-by-nextclade/17544 "2026-03-06T07:36:49Z")
Hello, I have a SARS-CoV-2 sequence analysis pipeline, one branch of which ends with pangolin and nextclade tests. When I take the same grouped fasta file and put it on the nextclade website and the nextclade galaxy too… --- ## [NCBI BLAST+ blastx and blastp cannot work with new nr\_2025-12-03](https://help.galaxyproject.org/t/ncbi-blast-blastx-and-blastp-cannot-work-with-new-nr-2025-12-03/16594)
**Author:** [@mmnashrullah](https://help.galaxyproject.org/u/mmnashrullah)\ **Replies:** 2\ **Last updated:** [February 28, 2026, 4:45am UTC](https://help.galaxyproject.org/t/ncbi-blast-blastx-and-blastp-cannot-work-with-new-nr-2025-12-03/16594 "2026-02-28T04:45:23Z")
Hi All, I got problem with NCBI BLAST+ blastx and blastp (and maybe other like tblastn and tblastx). I aware that we got new database nr\_2025-12-03. However, executing this at usegalaxy.eu led to this error. BLAST Data… --- ## [Troubleshooting failed sequence alignment (Sanger)](https://help.galaxyproject.org/t/troubleshooting-failed-sequence-alignment-sanger/16335)
**Author:** [@ground\_pearl\_girl](https://help.galaxyproject.org/u/ground_pearl_girl)\ **Replies:** 5\ **Last updated:** [February 28, 2026, 4:25am UTC](https://help.galaxyproject.org/t/troubleshooting-failed-sequence-alignment-sanger/16335 "2026-02-28T04:25:32Z")
Hi, I’ve been adapting this tutorial (Hands-on: Clean and manage Sanger sequences from raw files to aligned consensus / Clean and manage Sanger sequences from raw files to aligned consensus / Sequence analysis) to my own… --- ## [iPHoP 1.4.2 – Cannot select database](https://help.galaxyproject.org/t/iphop-1-4-2-cannot-select-database/17499)
**Author:** [@padk](https://help.galaxyproject.org/u/padk)\ **Replies:** 3\ **Last updated:** [February 27, 2026, 8:03am UTC](https://help.galaxyproject.org/t/iphop-1-4-2-cannot-select-database/17499 "2026-02-27T08:03:16Z")
Hi all, I’m trying to use the newest version of iPHoP (1.4.2) on Galaxy EU, but I’m unable to select a database. The database selection field displays: “No options available.” Interestingly, in the older version (1.… --- ## [Troubleshooting: qiime2 feature-classifier fit-classifier-naive-bayes](https://help.galaxyproject.org/t/troubleshooting-qiime2-feature-classifier-fit-classifier-naive-bayes/17493)
**Author:** [@ARW-UBT](https://help.galaxyproject.org/u/ARW-UBT)\ **Replies:** 4\ **Last updated:** [February 26, 2026, 7:42am UTC](https://help.galaxyproject.org/t/troubleshooting-qiime2-feature-classifier-fit-classifier-naive-bayes/17493 "2026-02-26T07:42:15Z")
Hello, I have sent an error report 11ac94870d0bb33ad2018af257e57a4a from within usegalaxy.eu. Am I supposed to post this request here again, or has this technical support request already registered at usegalaxy.eu? The… --- ## [Kraken2 Database Addition GTDB v220](https://help.galaxyproject.org/t/kraken2-database-addition-gtdb-v220/16461)
**Author:** [@Jon\_Colman](https://help.galaxyproject.org/u/Jon_Colman)\ **Replies:** 5\ **Last updated:** [November 5, 2025, 9:33pm UTC](https://help.galaxyproject.org/t/kraken2-database-addition-gtdb-v220/16461 "2025-11-05T21:33:40Z")
Is there any possibility of adding the GTDB v220 database to Kraken2??? Also the EupathDB 46 would be helpful. --- ## [Shovill producing blank contig graph file: Use Galaxy Version 1.1.0+galaxy2](https://help.galaxyproject.org/t/shovill-producing-blank-contig-graph-file-use-galaxy-version-1-1-0-galaxy2/17470)
**Author:** [@maria\_rosa](https://help.galaxyproject.org/u/maria_rosa)\ **Replies:** 7\ **Last updated:** [February 25, 2026, 9:46pm UTC](https://help.galaxyproject.org/t/shovill-producing-blank-contig-graph-file-use-galaxy-version-1-1-0-galaxy2/17470 "2026-02-25T21:46:23Z")
Some of my students and I have tried running Shovill on multiple files, and it is currently producing a blank contig graph file. I have generated this file successfully in the past, so there may be an issue with the curr… --- ## [Qiime2 Import 2025.10 errors: Standardize your fastq sequence names](https://help.galaxyproject.org/t/qiime2-import-2025-10-errors-standardize-your-fastq-sequence-names/16577)
**Author:** [@jln1137](https://help.galaxyproject.org/u/jln1137)\ **Replies:** 7\ **Last updated:** [February 25, 2026, 9:24pm UTC](https://help.galaxyproject.org/t/qiime2-import-2025-10-errors-standardize-your-fastq-sequence-names/16577 "2026-02-25T21:24:12Z")
Usegalaxy.eu has updated qiime2 to 2025.10, but this release has some problems with paired data affecting import and demux. Wondering if any fixes are on the horizon or if anyone is still running 2025.7. --- ## [Built-in reference dataset dada2 is missing](https://help.galaxyproject.org/t/built-in-reference-dataset-dada2-is-missing/4359)
**Author:** [@gjc](https://help.galaxyproject.org/u/gjc)\ **Replies:** 2\ **Last updated:** [February 25, 2026, 7:06pm UTC](https://help.galaxyproject.org/t/built-in-reference-dataset-dada2-is-missing/4359 "2026-02-25T19:06:51Z")
There is no built-in reference dataset when using the dada2: assignTaxonomy and Addspecies tool. How can I solve this? --- ## [Blast is not returning taxonomy results: Fetch Taxonomic Ranks](https://help.galaxyproject.org/t/blast-is-not-returning-taxonomy-results-fetch-taxonomic-ranks/17471)
**Author:** [@SAlves](https://help.galaxyproject.org/u/SAlves)\ **Replies:** 8\ **Last updated:** [February 24, 2026, 6:24pm UTC](https://help.galaxyproject.org/t/blast-is-not-returning-taxonomy-results-fetch-taxonomic-ranks/17471 "2026-02-24T18:24:00Z")
Dear Galaxy, I have been trying to run blast+ blast n with taxonomy results for scientific and comon name against the NCBI NT (2025), but it returns N/A on those fields. Tested a re-run on files from last week where it… --- ## [remuRNA Fatal error: Exit code 127 ()](https://help.galaxyproject.org/t/remurna-fatal-error-exit-code-127/17494)
**Author:** [@Nik](https://help.galaxyproject.org/u/Nik)\ **Replies:** 1\ **Last updated:** [February 24, 2026, 6:04pm UTC](https://help.galaxyproject.org/t/remurna-fatal-error-exit-code-127/17494 "2026-02-24T18:04:10Z")
In recent days, any job using the remuRNA tool has resulted in a Standard Error /data/jwd07/main/097/200/97200158/tool\_script.sh: line 22: python: command not found Job Messages: desc: Fatal error: Exit code 127 () er… --- ## [From Peaks To Genes Tutorial UCSC Main Errord](https://help.galaxyproject.org/t/from-peaks-to-genes-tutorial-ucsc-main-errord/17464)
**Author:** [@abdulrhman-abduallah](https://help.galaxyproject.org/u/abdulrhman-abduallah)\ **Replies:** 1\ **Last updated:** [February 17, 2026, 9:20am UTC](https://help.galaxyproject.org/t/from-peaks-to-genes-tutorial-ucsc-main-errord/17464 "2026-02-17T09:20:19Z")
Hi everyone, I am following the tutorial from peaks to genes however when I send the data to galaxy it gives this error and the brief description says the below picture in red, what to do in this case? thanks … --- ## [PLINK bed/bim/fam files are only downloadable as html/tabular/text files](https://help.galaxyproject.org/t/plink-bed-bim-fam-files-are-only-downloadable-as-html-tabular-text-files/17456)
**Author:** [@Andrea\_Trigueros](https://help.galaxyproject.org/u/Andrea_Trigueros)\ **Replies:** 3\ **Last updated:** [February 16, 2026, 5:51pm UTC](https://help.galaxyproject.org/t/plink-bed-bim-fam-files-are-only-downloadable-as-html-tabular-text-files/17456 "2026-02-16T17:51:41Z")
Hello, after running PLINK it produces output files bed, bim, fam, and log. However, when viewing these files in the History they appear as html, tab, txt, and txt files respectively. When looking at the Details→ Dataset… --- ## [PICRUSt2 Metagenome prediction](https://help.galaxyproject.org/t/picrust2-metagenome-prediction/17431)
**Author:** [@Peter\_Janampa](https://help.galaxyproject.org/u/Peter_Janampa)\ **Replies:** 3\ **Last updated:** [February 12, 2026, 8:06pm UTC](https://help.galaxyproject.org/t/picrust2-metagenome-prediction/17431 "2026-02-12T20:06:49Z")
Hello, is there an example of an input based on the shared format? Specifically, should the shared file also contain FASTA sequences? --- ## [Problem on Picrust2 webtool, even with tutorial files](https://help.galaxyproject.org/t/problem-on-picrust2-webtool-even-with-tutorial-files/11412)
**Author:** [@Mad.rien](https://help.galaxyproject.org/u/Mad.rien)\ **Replies:** 10\ **Last updated:** [February 12, 2026, 8:05pm UTC](https://help.galaxyproject.org/t/problem-on-picrust2-webtool-even-with-tutorial-files/11412 "2026-02-12T20:05:53Z")
Hello, I tried to use the webtool Picrust2, however even by using the tutorial fasta and biom files available at this adress (http://kronos.pharmacology.dal.ca/public\_files/picrust/picrust2\_tutorial\_files/chemerin\_16S.… [Previous page](https://help.galaxyproject.org/c/usegalaxy-eu-support/6.md?page=3) [Next page](https://help.galaxyproject.org/c/usegalaxy-eu-support/6.md?page=5)