# \#tool-help **URL:** https://help.galaxyproject.org/tag/tool-help/390.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [FAQ: Create a Qiime2 qza artifact from a Galaxy collection in ONE STEP!](https://help.galaxyproject.org/t/faq-create-a-qiime2-qza-artifact-from-a-galaxy-collection-in-one-step/17506)
**Author:** [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Replies:** 0\ **Last updated:** [February 25, 2026, 9:06pm UTC](https://help.galaxyproject.org/t/faq-create-a-qiime2-qza-artifact-from-a-galaxy-collection-in-one-step/17506 "2026-02-25T21:06:11Z")
:partying\_face: Try the new QZA creation method! Creating a Qiime2 qza artifact :magic\_wand: directly from a Galaxy Collection 1. Create your Galaxy Collection! Single end will have the collection shape List Paired end… --- ## [Progressive MAUVE](https://help.galaxyproject.org/t/progressive-mauve/18528)
**Author:** [@alexander.indra](https://help.galaxyproject.org/u/alexander.indra)\ **Replies:** 0\ **Last updated:** [October 22, 2026, 12:37pm UTC](https://help.galaxyproject.org/t/progressive-mauve/18528 "2026-10-22T12:37:13Z")
Hi, I’m a long-time but infrequent Galaxy user, and I always end up getting lost because Galaxy assigns generic identifiers to the output files. I’m currently having this problem with progressiveMauve and its output fi… --- ## [Trinity read normalization](https://help.galaxyproject.org/t/trinity-read-normalization/18527)
**Author:** [@analaura1202](https://help.galaxyproject.org/u/analaura1202)\ **Replies:** 0\ **Last updated:** [October 22, 2026, 8:51am UTC](https://help.galaxyproject.org/t/trinity-read-normalization/18527 "2026-10-22T08:51:53Z")
Hello! I have a Trinity de novo assembly, and I would like to use the Trinity-normalized reads as input for rnaSPAdes so I can compare the two assemblies. Do you know how I could do this in Galaxy? Thanks! --- ## [DIA-NN input error](https://help.galaxyproject.org/t/dia-nn-input-error/18524)
**Author:** [@lebogang](https://help.galaxyproject.org/u/lebogang)\ **Replies:** 1\ **Last updated:** [October 22, 2026, 12:00am UTC](https://help.galaxyproject.org/t/dia-nn-input-error/18524 "2026-10-22T00:00:41Z")
Hello support, I am running DIA-NN 1.8.1+galaxy5 with Bruker timsTOF .d datasets uploaded as brukertdf.d.tar. The job fails during input extraction, before DIA-NN starts. The wrapper runs tar -xf ... -C ./input\_data an… --- ## [PharmCAT (and its VCF preprocessor)](https://help.galaxyproject.org/t/pharmcat-and-its-vcf-preprocessor/18501)
**Author:** [@qcsciphi](https://help.galaxyproject.org/u/qcsciphi)\ **Replies:** 0\ **Last updated:** [October 19, 2026, 2:29pm UTC](https://help.galaxyproject.org/t/pharmcat-and-its-vcf-preprocessor/18501 "2026-10-19T14:29:25Z")
Dear Galaxy Europe team, The PharmCAT link below states that the input VCF must be “prepared” either by the user or by PharmCAT’s VCF Preprocessor tool. As there’s no info about the preporcessor in the tool description… --- ## [ConFindr - cannot find E. coli MLST](https://help.galaxyproject.org/t/confindr-cannot-find-e-coli-mlst/18484)
**Author:** [@anneliesvb](https://help.galaxyproject.org/u/anneliesvb)\ **Replies:** 1\ **Last updated:** [October 16, 2026, 11:50pm UTC](https://help.galaxyproject.org/t/confindr-cannot-find-e-coli-mlst/18484 "2026-10-16T23:50:33Z")
--- ## [Parabricks fq2bam](https://help.galaxyproject.org/t/parabricks-fq2bam/18485)
**Author:** [@numbergirl86](https://help.galaxyproject.org/u/numbergirl86)\ **Replies:** 3\ **Last updated:** [October 16, 2026, 5:54pm UTC](https://help.galaxyproject.org/t/parabricks-fq2bam/18485 "2026-10-16T17:54:12Z")
Is the ability to use a reference genome from history going to be added to this tool at some point? --- ## [Tiberius indexes missing? How to navigate tool versions to find them!](https://help.galaxyproject.org/t/tiberius-indexes-missing-how-to-navigate-tool-versions-to-find-them/18468)
**Author:** [@thobile.bolt](https://help.galaxyproject.org/u/thobile.bolt)\ **Replies:** 2\ **Last updated:** [October 14, 2026, 6:24pm UTC](https://help.galaxyproject.org/t/tiberius-indexes-missing-how-to-navigate-tool-versions-to-find-them/18468 "2026-10-14T18:24:41Z")
Unable to run Tiberius, model required. --- ## [Help with IQ tree](https://help.galaxyproject.org/t/help-with-iq-tree/18464)
**Author:** [@Katherine\_Gonzalez](https://help.galaxyproject.org/u/Katherine_Gonzalez)\ **Replies:** 3\ **Last updated:** [October 14, 2026, 6:19pm UTC](https://help.galaxyproject.org/t/help-with-iq-tree/18464 "2026-10-14T18:19:31Z")
my Mafft file is unable to create an IQ tree. Any ideas on how to help? --- ## [MiRDeep2\_no\_inbuilt\_reference\_genome(whitespace issue with file uploaded)](https://help.galaxyproject.org/t/mirdeep2-no-inbuilt-reference-genome-whitespace-issue-with-file-uploaded/18439)
**Author:** [@nive3437](https://help.galaxyproject.org/u/nive3437)\ **Replies:** 1\ **Last updated:** [October 6, 2026, 11:51pm UTC](https://help.galaxyproject.org/t/mirdeep2-no-inbuilt-reference-genome-whitespace-issue-with-file-uploaded/18439 "2026-10-06T23:51:53Z")
Please provide the built-in reference genome, as we are facing an issue with the uploaded reference genome (white space issue) in miRdeep2 --- ## [NUCmer/MUMmer dotplot job exceeds memory allocation for ~1 Gb alligator gar genomes](https://help.galaxyproject.org/t/nucmer-mummer-dotplot-job-exceeds-memory-allocation-for-1-gb-alligator-gar-genomes/18445)
**Author:** [@micjwol](https://help.galaxyproject.org/u/micjwol)\ **Replies:** 1\ **Last updated:** [October 6, 2026, 11:45pm UTC](https://help.galaxyproject.org/t/nucmer-mummer-dotplot-job-exceeds-memory-allocation-for-1-gb-alligator-gar-genomes/18445 "2026-10-06T23:45:24Z")
I am using Galaxy to compare two whole-genome assemblies of alligator gar (Atractosteus spatula) as part of a male-versus-female genome comparison. The two FASTA assemblies are: - Reference / male: MaleAlligatorGar\_fAt… --- ## [miRge3 reference library not available in the server](https://help.galaxyproject.org/t/mirge3-reference-library-not-available-in-the-server/18424)
**Author:** [@nive3437](https://help.galaxyproject.org/u/nive3437)\ **Replies:** 8\ **Last updated:** [October 5, 2026, 5:43pm UTC](https://help.galaxyproject.org/t/mirge3-reference-library-not-available-in-the-server/18424 "2026-10-05T17:43:37Z")
Admins, please fix the following issue I’m trying to use the miRge3 pipeline for miRNA seq analyses (done using the MGI platform), the miRge3 human library is not available (nor can it be manually uploaded) --- ## [Panaroo 1.8.0+galaxy0 fails on GFF3 collection with FileNotFoundError: input\_directory/\*.gff](https://help.galaxyproject.org/t/panaroo-1-8-0-galaxy0-fails-on-gff3-collection-with-filenotfounderror-input-directory-gff/18269)
**Author:** [@Loc\_Le](https://help.galaxyproject.org/u/Loc_Le)\ **Replies:** 7\ **Last updated:** [September 28, 2026, 5:59pm UTC](https://help.galaxyproject.org/t/panaroo-1-8-0-galaxy0-fails-on-gff3-collection-with-filenotfounderror-input-directory-gff/18269 "2026-09-28T17:59:43Z")
Hello, I encountered what appears to be a wrapper issue in Panaroo (Galaxy wrapper version 1.8.0+galaxy0 on usegalaxy.eu). Input: - Collection of 19 GFF3 files - All files were generated by Bakta - Collection dataty… --- ## [BEAST2 tool fails with ClassNotFoundException on Galaxy](https://help.galaxyproject.org/t/beast2-tool-fails-with-classnotfoundexception-on-galaxy/18414)
**Author:** [@Sawar](https://help.galaxyproject.org/u/Sawar)\ **Replies:** 1\ **Last updated:** [September 23, 2026, 6:08pm UTC](https://help.galaxyproject.org/t/beast2-tool-fails-with-classnotfoundexception-on-galaxy/18414 "2026-09-23T18:08:55Z")
Continuing the discussion from Installation of BEAST on Galaxy Europe: Dear Galaxy Europe team, I’m trying to run the BEAST2 tool on usegalaxy.eu and the job fails immediately, before the analysis starts. The same XML … --- ## [Funannotate BUSCO models - mucorales missing](https://help.galaxyproject.org/t/funannotate-busco-models-mucorales-missing/18386)
**Author:** [@Sydney\_Harned](https://help.galaxyproject.org/u/Sydney_Harned)\ **Replies:** 1\ **Last updated:** [September 14, 2026, 5:54pm UTC](https://help.galaxyproject.org/t/funannotate-busco-models-mucorales-missing/18386 "2026-09-14T17:54:43Z")
Hi Galaxy team, I’m running the “Funannotate predict annotation” tool and the “BUSCO models to align” dropdown only shows Dikarya as an option. Could you please add mucorales\_odb10 to the available lineages for this too… --- ## [Confirmed and pending status: Tool "Retrieve bold" is not working : warning message + log](https://help.galaxyproject.org/t/confirmed-and-pending-status-tool-retrieve-bold-is-not-working-warning-message-log/18369)
**Author:** [@eline.jkn](https://help.galaxyproject.org/u/eline.jkn)\ **Replies:** 2\ **Last updated:** [September 7, 2026, 9:37pm UTC](https://help.galaxyproject.org/t/confirmed-and-pending-status-tool-retrieve-bold-is-not-working-warning-message-log/18369 "2026-09-07T21:37:39Z")
Does not work, always same error: Tool standard error : Warning message: In data.table::fread(text = x, header = header, sep = sep, ...) : Stopped early on line 44. Expected 2 fields but found 0. Consider fill=TRUE a… --- ## [Prodigal Gene Predictor: error option (# Other genetic codes 1-25) stderr Invalid translation table specified](https://help.galaxyproject.org/t/prodigal-gene-predictor-error-option-other-genetic-codes-1-25-stderr-invalid-translation-table-specified/18350)
**Author:** [@tvtv195](https://help.galaxyproject.org/u/tvtv195)\ **Replies:** 1\ **Last updated:** [September 7, 2026, 5:55pm UTC](https://help.galaxyproject.org/t/prodigal-gene-predictor-error-option-other-genetic-codes-1-25-stderr-invalid-translation-table-specified/18350 "2026-09-07T17:55:12Z")
I am experiencing a bug in this specific version of the Galaxy wrapper (Galaxy Version 2.6.3+galaxy0). The developer forgot to link the conditional text field container to the # : Other genetic codes 1-25 selection choi… --- ## [STARsolo custom reference fails during genomeGenerate — need genomeChrBinNbits for fragmented Nicotiana genome](https://help.galaxyproject.org/t/starsolo-custom-reference-fails-during-genomegenerate-need-genomechrbinnbits-for-fragmented-nicotiana-genome/18360)
**Author:** [@fforn](https://help.galaxyproject.org/u/fforn)\ **Replies:** 4\ **Last updated:** [September 3, 2026, 6:53pm UTC](https://help.galaxyproject.org/t/starsolo-custom-reference-fails-during-genomegenerate-need-genomechrbinnbits-for-fragmented-nicotiana-genome/18360 "2026-09-03T18:53:22Z")
Hi Galaxy Europe team, I am trying to reconstruct a published 10x Genomics v3 single-nucleus RNA-seq dataset from Nicotiana tabacum K326 using RNA STARsolo on singlecell.usegalaxy.eu. Tool: RNA STARsolo 2.7.11b+galaxy2 … --- ## [Dorado now missing from usegalaxy.eu site...?](https://help.galaxyproject.org/t/dorado-now-missing-from-usegalaxy-eu-site/18352)
**Author:** [@scyllas1981](https://help.galaxyproject.org/u/scyllas1981)\ **Replies:** 4\ **Last updated:** [September 3, 2026, 1:55am UTC](https://help.galaxyproject.org/t/dorado-now-missing-from-usegalaxy-eu-site/18352 "2026-09-03T01:55:48Z")
Hi all - hoping an admin usegalaxy.e.u could help Today I can’t seem to find dorado in the tools - has it been removed??? Have used recently, this seems a significant change if removed. Thanks Graham --- ## [Pre.cluster (mothur) empty outputs: consider using groups! Please see tutorial example](https://help.galaxyproject.org/t/pre-cluster-mothur-empty-outputs-consider-using-groups-please-see-tutorial-example/18347)
**Author:** [@Heba\_Hathout](https://help.galaxyproject.org/u/Heba_Hathout)\ **Replies:** 1\ **Last updated:** [August 27, 2026, 4:27pm UTC](https://help.galaxyproject.org/t/pre-cluster-mothur-empty-outputs-consider-using-groups-please-see-tutorial-example/18347 "2026-08-27T16:27:53Z")
Server URL: usegalaxy dot org I’m running the Pre.cluster tool (mothur, Galaxy Version 1.39.5.0) on a 16S mothur pipeline (23 samples, RedSeaSeawater\_16S\_Mothur pipeline history). The job has been stuck in “running” s… --- ## [Jobs stuck in 'new' state — Faster Download and Extract Reads in FASTQ](https://help.galaxyproject.org/t/jobs-stuck-in-new-state-faster-download-and-extract-reads-in-fastq/18337)
**Author:** [@Ghaida](https://help.galaxyproject.org/u/Ghaida)\ **Replies:** 4\ **Last updated:** [August 25, 2026, 12:12pm UTC](https://help.galaxyproject.org/t/jobs-stuck-in-new-state-faster-download-and-extract-reads-in-fastq/18337 "2026-08-25T12:12:55Z")
Resolved :white\_check\_mark: Tool name: “Faster Download and Extract Reads in FASTQ format from NCBI SRA (Galaxy Version 3.1.1+galaxy1)” Clicking Run Tool shows ‘please wait’ for under a second, then reverts with no job… --- ## [HUMAnN Collection Mapping Launch Failure](https://help.galaxyproject.org/t/humann-collection-mapping-launch-failure/18290)
**Author:** [@Reki](https://help.galaxyproject.org/u/Reki)\ **Replies:** 1\ **Last updated:** [August 18, 2026, 5:50pm UTC](https://help.galaxyproject.org/t/humann-collection-mapping-launch-failure/18290 "2026-08-18T17:50:39Z")
HUMAnN 3.9 runs successfully on individual datasets using: Bowtie2 unaligned read pairs (collection 646) MetaPhlAn predicted taxon relative abundances (collection 945) bypass taxonomic profiling However, when selectin… --- ## [HUMAnN error version](https://help.galaxyproject.org/t/humann-error-version/18284)
**Author:** [@Reki](https://help.galaxyproject.org/u/Reki)\ **Replies:** 1\ **Last updated:** [August 14, 2026, 8:10pm UTC](https://help.galaxyproject.org/t/humann-error-version/18284 "2026-08-14T20:10:44Z")
Galaxy Microbiology HUMAnN 3.9+galaxy1 Error: "The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJun23" The only MetaPhlAn marker database available under “Locally cache… --- ## [Help ChewBBACA: using collection folders and NormalizeFasta to avoid "ValueError: This FASTA file contains comments "](https://help.galaxyproject.org/t/help-chewbbaca-using-collection-folders-and-normalizefasta-to-avoid-valueerror-this-fasta-file-contains-comments/18278)
**Author:** [@msuh](https://help.galaxyproject.org/u/msuh)\ **Replies:** 5\ **Last updated:** [August 13, 2026, 7:43pm UTC](https://help.galaxyproject.org/t/help-chewbbaca-using-collection-folders-and-normalizefasta-to-avoid-valueerror-this-fasta-file-contains-comments/18278 "2026-08-13T19:43:15Z")
I am working through a training module (Step-by-step Tutorial - chewBBACA 3.5.4 documentation) using datasets provided. Whenever I input cgMLSTschema95.txt file as genes-list to do “Allele calling with additional genome… --- ## ["Invalid storage location" when trying to move data to Backblaze B2](https://help.galaxyproject.org/t/invalid-storage-location-when-trying-to-move-data-to-backblaze-b2/18276)
**Author:** [@Peter\_van\_Heusden](https://help.galaxyproject.org/u/Peter_van_Heusden)\ **Replies:** 5\ **Last updated:** [August 12, 2026, 10:30am UTC](https://help.galaxyproject.org/t/invalid-storage-location-when-trying-to-move-data-to-backblaze-b2/18276 "2026-08-12T10:30:55Z")
I’m trying to move the datasets in a history (8228344521d4e949) to my Backblaze B2 storage but when I try and do this with the “Manage storage location” option, I get told that “The selected storage location is not avail… --- ## [ABRicate databases and tool versions in workflows](https://help.galaxyproject.org/t/abricate-databases-and-tool-versions-in-workflows/18216)
**Author:** [@Sarah\_Teichman](https://help.galaxyproject.org/u/Sarah_Teichman)\ **Replies:** 3\ **Last updated:** [August 11, 2026, 6:31pm UTC](https://help.galaxyproject.org/t/abricate-databases-and-tool-versions-in-workflows/18216 "2026-08-11T18:31:10Z")
Hi, I would like to use ABRicate with the bacmet2 database, and when I run ABRicate List in Galaxy it lists 12 available databases, including bacmet2, but when I look at the workflow for ABRicate itself, under advanced o… --- ## [Notebooks: more about memory resources and HTP analysis](https://help.galaxyproject.org/t/notebooks-more-about-memory-resources-and-htp-analysis/18267)
**Author:** [@0808](https://help.galaxyproject.org/u/0808)\ **Replies:** 2\ **Last updated:** [August 11, 2026, 7:31am UTC](https://help.galaxyproject.org/t/notebooks-more-about-memory-resources-and-htp-analysis/18267 "2026-08-11T07:31:33Z")
Title: Request for higher-memory resource for RSEM v1.3.1 due to OOM Hello Galaxy Europe Support Team, I am reprocessing the public PRJEB40416 gastric cancer RNA-seq dataset on usegalaxy.eu. STAR alignment has comple… --- ## [Interactive JupyterLab Notebook - use terminal for RNA-seq alignment](https://help.galaxyproject.org/t/interactive-jupyterlab-notebook-use-terminal-for-rna-seq-alignment/18055)
**Author:** [@cventophd](https://help.galaxyproject.org/u/cventophd)\ **Replies:** 1\ **Last updated:** [August 10, 2026, 8:19pm UTC](https://help.galaxyproject.org/t/interactive-jupyterlab-notebook-use-terminal-for-rna-seq-alignment/18055 "2026-08-10T20:19:06Z")
Hello, I would like to try an experiment where I use the CLI in Galaxy via Interactive JupyterLab Notebook to do an RNA-seq alignment using histat2 or STAR. However, whenever I use either these in the terminal I get “co… --- ## [Busco string\_type error](https://help.galaxyproject.org/t/busco-string-type-error/18060)
**Author:** [@Joseph\_Kogan](https://help.galaxyproject.org/u/Joseph_Kogan)\ **Replies:** 1\ **Last updated:** [August 10, 2026, 7:17pm UTC](https://help.galaxyproject.org/t/busco-string-type-error/18060 "2026-08-10T19:17:43Z")
I am trying to run BUSCO on a protein fasta file generated from a gff3 annotation, which has worked without a hitch in the past. This time, no matter what I do and regardless of the fact that I am using the exact same to… --- ## [GTDB-Tk, reference data, and job queues: leave jobs queued for this competitive cluster group!](https://help.galaxyproject.org/t/gtdb-tk-reference-data-and-job-queues-leave-jobs-queued-for-this-competitive-cluster-group/18237)
**Author:** [@horikini](https://help.galaxyproject.org/u/horikini)\ **Replies:** 3\ **Last updated:** [August 10, 2026, 6:21pm UTC](https://help.galaxyproject.org/t/gtdb-tk-reference-data-and-job-queues-leave-jobs-queued-for-this-competitive-cluster-group/18237 "2026-08-10T18:21:52Z")
Hi, I have a GTDB-Tk classify\_wf job that has been stuck in “queued” state (never transitioned to “running”) for over 73 hours. Job ID: 4838ba20a6d86765aad1b932f8f80dd1 Tool: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk\_cl… [Next page](https://help.galaxyproject.org/tag/tool-help/390.md?match_all_tags=true&page=1&tags%5B%5D=tool-help)