# \#tool-deprecated **URL:** https://help.galaxyproject.org/tag/tool-deprecated/163.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Fatal error: using trinity](https://help.galaxyproject.org/t/fatal-error-using-trinity/10218)
**Author:** [@guser](https://help.galaxyproject.org/u/guser)\ **Replies:** 2\ **Last updated:** [April 18, 2026, 2:32am UTC](https://help.galaxyproject.org/t/fatal-error-using-trinity/10218 "2026-04-18T02:32:45Z")
Hi I am using trinity and the error message is: "Fatal error: Exit code 1 () cp: -r not specified; omitting directory ‘trinity\_out\_dir/Trinity.tmp.fasta.salmon.idx’ /ocean/projects/mcb140028p/xcgalaxy/main/staging/50… --- ## [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 … --- ## [TRINITY run time](https://help.galaxyproject.org/t/trinity-run-time/2814)
**Author:** [@ASHISH\_MISHRA](https://help.galaxyproject.org/u/ASHISH_MISHRA)\ **Replies:** 2\ **Last updated:** [April 8, 2026, 2:26am UTC](https://help.galaxyproject.org/t/trinity-run-time/2814 "2026-04-08T02:26:07Z")
I am trying to assembled data using TRINITY. It has been well over 24hrs and it still shows that the analysis job is still running. Is that normal? --- ## [Trinotate error SQLite](https://help.galaxyproject.org/t/trinotate-error-sqlite/17607)
**Author:** [@kamran.azim](https://help.galaxyproject.org/u/kamran.azim)\ **Replies:** 3\ **Last updated:** [April 8, 2026, 2:14am UTC](https://help.galaxyproject.org/t/trinotate-error-sqlite/17607 "2026-04-08T02:14:50Z")
Error, cmd: wget "http://eggnogdb.embl.de/download/eggnog\_4.5/data/NOG/NOG.annotations.tsv.gz" died with ret 2048 at /usr/local/lib/site\_perl/5.26.2/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0x55e4f889f918)) … --- ## [Trinotate error? See GTN Transcriptomics tutorials for alternatives!](https://help.galaxyproject.org/t/trinotate-error-see-gtn-transcriptomics-tutorials-for-alternatives/16353)
**Author:** [@igor](https://help.galaxyproject.org/u/igor)\ **Replies:** 4\ **Last updated:** [April 8, 2026, 2:14am UTC](https://help.galaxyproject.org/t/trinotate-error-see-gtn-transcriptomics-tutorials-for-alternatives/16353 "2026-04-08T02:14:14Z")
GDay, Trinotate jobs fail in Europe and Australia, with similar message: .import Trinotate.TaxonomyIndex TaxonomyIndex" | sqlite3 Trinotate.sqlite \* Running CMD: wget "http://eggnogdb.embl.de/download/eggnog\_4.5/data/N… --- ## [Trinotate SQLite boilerplate unavailable on usegalaxy.eu?](https://help.galaxyproject.org/t/trinotate-sqlite-boilerplate-unavailable-on-usegalaxy-eu/15953)
**Author:** [@mmnashrullah](https://help.galaxyproject.org/u/mmnashrullah)\ **Replies:** 4\ **Last updated:** [April 8, 2026, 2:13am UTC](https://help.galaxyproject.org/t/trinotate-sqlite-boilerplate-unavailable-on-usegalaxy-eu/15953 "2026-04-08T02:13:53Z")
Hi All, I am trying Trinotate for my annotation. However, I found that the link https://data.broadinstitute.org/Trinity/\_\_deprecated\_trinotate\_resources/Trinotate\_v3\_RESOURCES/Trinotate\_v3.sqlite.gz is dead so we cannot… --- ## [Trinotate error resulting in "The job creating this dataset has been resubmitted"](https://help.galaxyproject.org/t/trinotate-error-resulting-in-the-job-creating-this-dataset-has-been-resubmitted/6187)
**Author:** [@jaredbernard](https://help.galaxyproject.org/u/jaredbernard)\ **Replies:** 11\ **Last updated:** [April 8, 2026, 2:10am UTC](https://help.galaxyproject.org/t/trinotate-error-resulting-in-the-job-creating-this-dataset-has-been-resubmitted/6187 "2026-04-08T02:10:49Z")
I ran into this error when running Trinotate on Galaxy Europe: The job creating this dataset has been resubmitted An error occurred with this dataset: This job was resubmitted to the queue because it encountered a to… --- ## [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… --- ## [Deprecated tool: Trinonate. See GTN Transcriptomics tutorials for alternatives](https://help.galaxyproject.org/t/deprecated-tool-trinonate-see-gtn-transcriptomics-tutorials-for-alternatives/12392)
**Author:** [@Ravita\_Tadiya](https://help.galaxyproject.org/u/Ravita_Tadiya)\ **Replies:** 2\ **Last updated:** [April 8, 2026, 2:04am UTC](https://help.galaxyproject.org/t/deprecated-tool-trinonate-see-gtn-transcriptomics-tutorials-for-alternatives/12392 "2026-04-08T02:04:22Z")
Error, no gene\_id for trans: \[TRINITY\_DN76711\_c0\_g1\_i1\] at /mnt/tools/tool\_dependencies/\_conda/envs/mulled-v1-0534adab201f5820009b76442004c506252b49a190f1c3ca55d89fa4eb5bd895/bin/TrinotateSeqLoader.pl line 132, \<$fileha… --- ## [How to use Trinotate output?](https://help.galaxyproject.org/t/how-to-use-trinotate-output/3009)
**Author:** [@YKV](https://help.galaxyproject.org/u/YKV)\ **Replies:** 2\ **Last updated:** [April 8, 2026, 1:53am UTC](https://help.galaxyproject.org/t/how-to-use-trinotate-output/3009 "2026-04-08T01:53:24Z")
Hi, I have used genes to transcript map, trinity, transdecoder. And used those output files as input in Trinotate. And haven’t filled blastx/blastp/hmmer fields as it said optional. I tried to do blastx/p/hmmer but some… --- ## [Project help...(variant analysis)](https://help.galaxyproject.org/t/project-help-variant-analysis/3853)
**Author:** [@karp05](https://help.galaxyproject.org/u/karp05)\ **Replies:** 2\ **Last updated:** [April 8, 2026, 1:41am UTC](https://help.galaxyproject.org/t/project-help-variant-analysis/3853 "2026-04-08T01:41:53Z")
Hi, (note: I am an absolute complete beginner in this) Ive recently been taking a course on coursera about using galaxy and I have a project whereby I have to "Create a Galaxy workflow to identify polymorphic sites in … --- ## [Need help with selecting reference genome in Galaxy installed locally](https://help.galaxyproject.org/t/need-help-with-selecting-reference-genome-in-galaxy-installed-locally/4931)
**Author:** [@manojmw](https://help.galaxyproject.org/u/manojmw)\ **Replies:** 3\ **Last updated:** [April 8, 2026, 1:41am UTC](https://help.galaxyproject.org/t/need-help-with-selecting-reference-genome-in-galaxy-installed-locally/4931 "2026-04-08T01:41:17Z")
Hello everyone, I am trying to annotate a VCF file containing the sample data to predict the genes with polymorphic sites. I am using ANNOVAR tool. But, no options are available for me under Gene/Annotation/Databases in… --- ## [Annotate VCF with gene names](https://help.galaxyproject.org/t/annotate-vcf-with-gene-names/3153)
**Author:** [@yahia.elshabrawy](https://help.galaxyproject.org/u/yahia.elshabrawy)\ **Replies:** 4\ **Last updated:** [April 8, 2026, 1:40am UTC](https://help.galaxyproject.org/t/annotate-vcf-with-gene-names/3153 "2026-04-08T01:40:46Z")
Im trying to add annotations to a vcf file. I had paired-end reads of 3 individuals, I aligned each pair to the human hg19 genome, then I generated the VCF file using FreeBayes to call for variants of the 3 sets of data… --- ## [ANNOVAR error message biomina](https://help.galaxyproject.org/t/annovar-error-message-biomina/1772)
**Author:** [@A\_Van](https://help.galaxyproject.org/u/A_Van)\ **Replies:** 4\ **Last updated:** [April 8, 2026, 1:39am UTC](https://help.galaxyproject.org/t/annovar-error-message-biomina/1772 "2026-04-08T01:39:47Z")
Hi! I’m a beginner in Galaxy. I have tried several times, in different days, to run a job with ANNOVAR on biomina, but the job was failed. This message appeared: Job cannot be completed due to a cluster error, please ret… --- ## [Unable to use 'ANNOVAR Annotate VCF' to annotate my vcf file](https://help.galaxyproject.org/t/unable-to-use-annovar-annotate-vcf-to-annotate-my-vcf-file/6431)
**Author:** [@Abieskawa](https://help.galaxyproject.org/u/Abieskawa)\ **Replies:** 2\ **Last updated:** [April 8, 2026, 1:38am UTC](https://help.galaxyproject.org/t/unable-to-use-annovar-annotate-vcf-to-annotate-my-vcf-file/6431 "2026-04-08T01:38:55Z")
Hello everyone. I want to annotate my vcf file and transfer it to tabular, so I can count the gene that content mutation maximum in number. When I use ANNOVAR Annotate VCF to annotate my vcf file, I cannot choose the ann… --- ## [ANNOVAR annotation error](https://help.galaxyproject.org/t/annovar-annotation-error/2730)
**Author:** [@umagaur](https://help.galaxyproject.org/u/umagaur)\ **Replies:** 2\ **Last updated:** [April 8, 2026, 1:38am UTC](https://help.galaxyproject.org/t/annovar-annotation-error/2730 "2026-04-08T01:38:30Z")
Hi, I am getting the following error message when I am trying to run ANNOVAR annotation on a vcf file in order to identify genes with polymorphic sites; WARNING to old ANNOVAR users: this program no longer does line-to-… --- ## [ANNOVAR 0 lines result](https://help.galaxyproject.org/t/annovar-0-lines-result/2969)
**Author:** [@ThibautMatis](https://help.galaxyproject.org/u/ThibautMatis)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 1:38am UTC](https://help.galaxyproject.org/t/annovar-0-lines-result/2969 "2026-04-08T01:38:01Z")
Hi, I’m a beginner on Galaxy and I’m trying to use ANNOVAR on VCF files from exome (it’s all I have). Variant caller used was Samtool. VCF files have been mapped on hg19, and I filled this information when I imported my … --- ## [Annovar on galaxy v0.2 not working](https://help.galaxyproject.org/t/annovar-on-galaxy-v0-2-not-working/6796)
**Author:** [@aradhna](https://help.galaxyproject.org/u/aradhna)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 1:36am UTC](https://help.galaxyproject.org/t/annovar-on-galaxy-v0-2-not-working/6796 "2026-04-08T01:36:44Z")
Hello, I have to finish a project for an online course where I need to identify DNA polymorphic sites through galaxy. I want to annotate vcf file generated after free Bayes step. I am new to this analysis part and I hav… --- ## [On obtaining current eggNOG data](https://help.galaxyproject.org/t/on-obtaining-current-eggnog-data/16000)
**Author:** [@mmnashrullah](https://help.galaxyproject.org/u/mmnashrullah)\ **Replies:** 1\ **Last updated:** [July 22, 2025, 7:38pm UTC](https://help.galaxyproject.org/t/on-obtaining-current-eggnog-data/16000 "2025-07-22T19:38:06Z")
Hi All, After finally made it works, during the building of the Trinotate SQL Boilerplate, I found that one of the data sources is NOG annotations taken from eggNOG4.5. We know that current version of eggNOG is eggNOG … --- ## [Setup for Annovar](https://help.galaxyproject.org/t/setup-for-annovar/15032)
**Author:** [@casio](https://help.galaxyproject.org/u/casio)\ **Replies:** 4\ **Last updated:** [March 21, 2025, 2:58pm UTC](https://help.galaxyproject.org/t/setup-for-annovar/15032 "2025-03-21T14:58:46Z")
Hi, I try to setup ANNOVAR Annotate VCF with functional information using ANNOVAR(Galaxy Version 0.2) on a local Galaxy server running 24.2.3. As the tool README suggested, I downloaded the software and the databases, … --- ## [How to run MiXCR or AIRR-seq analysis](https://help.galaxyproject.org/t/how-to-run-mixcr-or-airr-seq-analysis/13028)
**Author:** [@Patrick\_Collins](https://help.galaxyproject.org/u/Patrick_Collins)\ **Replies:** 3\ **Last updated:** [July 24, 2024, 11:46pm UTC](https://help.galaxyproject.org/t/how-to-run-mixcr-or-airr-seq-analysis/13028 "2024-07-24T23:46:43Z")
Hi. I would like to analyze B cell receptor (BCR) and T cell receptor (TCR) recombination data on Galaxy. In the past I have used MiXCR via the command line. To use MiXCR, do I need to install the tool from the toolshed… --- ## [Trinity problems? Use rnaSPAdes instead!](https://help.galaxyproject.org/t/trinity-problems-use-rnaspades-instead/12023)
**Author:** [@Sutrisha\_Kundu](https://help.galaxyproject.org/u/Sutrisha_Kundu)\ **Replies:** 14\ **Last updated:** [April 13, 2024, 5:57am UTC](https://help.galaxyproject.org/t/trinity-problems-use-rnaspades-instead/12023 "2024-04-13T05:57:33Z")
Hello. I have tried to run Trinity for a de novo transcriptome assembly of RNA-Seq data that has been trimmed successfully using Trimmomatic but the job is still waiting to run. I have executed Trinity operation 48 hrs b… --- ## [Velvetoptimiser: long running or failed job? Try a SPAdes tool instead!](https://help.galaxyproject.org/t/velvetoptimiser-long-running-or-failed-job-try-a-spades-tool-instead/12046)
**Author:** [@Sutrisha\_Kundu](https://help.galaxyproject.org/u/Sutrisha_Kundu)\ **Replies:** 1\ **Last updated:** [March 29, 2024, 5:24pm UTC](https://help.galaxyproject.org/t/velvetoptimiser-long-running-or-failed-job-try-a-spades-tool-instead/12046 "2024-03-29T17:24:22Z")
Hello, I am performing a transcriptome de novo assembly using Velvetoptimiser. The Velvetoptimiser job is running from past 5 days. The job is still yellow and has never turned green. Is it stuck? Can you please help me… --- ## [Extract CuffDiff tool](https://help.galaxyproject.org/t/extract-cuffdiff-tool/11671)
**Author:** [@Ahmad\_Suparmin](https://help.galaxyproject.org/u/Ahmad_Suparmin)\ **Replies:** 1\ **Last updated:** [February 8, 2024, 6:30pm UTC](https://help.galaxyproject.org/t/extract-cuffdiff-tool/11671 "2024-02-08T18:30:16Z")
I can not find Extract CuffDiff tool in galaxy australia, so any help to find or alternative way to extract RNA-Seq SQLite result data? --- ## [Track height in trackster](https://help.galaxyproject.org/t/track-height-in-trackster/11176)
**Author:** [@Richard\_Naiberg](https://help.galaxyproject.org/u/Richard_Naiberg)\ **Replies:** 2\ **Last updated:** [November 20, 2023, 7:14pm UTC](https://help.galaxyproject.org/t/track-height-in-trackster/11176 "2023-11-20T19:14:37Z")
When a load a number of tracks, I can only see a sliver of the output. Here is one view here is another of the same output How can I see them all at the same time? --- ## [Trackster adding new tracks to visualisation](https://help.galaxyproject.org/t/trackster-adding-new-tracks-to-visualisation/138)
**Author:** [@janepuh](https://help.galaxyproject.org/u/janepuh)\ **Replies:** 3\ **Last updated:** [November 20, 2023, 10:25pm UTC](https://help.galaxyproject.org/t/trackster-adding-new-tracks-to-visualisation/138 "2023-11-20T22:25:51Z")
Hello, I’m using https://usegalaxy.org. I want to visualize 2 BAM-files from my history in 2 tracks in one visualisation in Trackster. I can create visualization with one of the files. But I can’t add a new track to sav… --- ## [Trackster not loading dataset with server indexed "database" assigned](https://help.galaxyproject.org/t/trackster-not-loading-dataset-with-server-indexed-database-assigned/2308)
**Author:** [@lgardie](https://help.galaxyproject.org/u/lgardie)\ **Replies:** 3\ **Last updated:** [January 14, 2020, 2:14am UTC](https://help.galaxyproject.org/t/trackster-not-loading-dataset-with-server-indexed-database-assigned/2308 "2020-01-14T02:14:46Z")
I have the same issue, but all my files have the same database/build (mm10). Even when I make new visualizations and want to add them to an already existing one, Galaxy says its not available and won’t let me click. Is t… --- ## [Trinity : use rnaSPAdes instead!](https://help.galaxyproject.org/t/trinity-use-rnaspades-instead/10737)
**Author:** [@Pedro](https://help.galaxyproject.org/u/Pedro)\ **Replies:** 4\ **Last updated:** [September 6, 2023, 4:31pm UTC](https://help.galaxyproject.org/t/trinity-use-rnaspades-instead/10737 "2023-09-06T16:31:48Z")
Hi, I am trying to run trinity on unaligned reads files generated by HISAT2. I have tried the following, after consulting other users quaries: directly with the files generated by HISAT2 after FASTQgroomer with defau… --- ## [Convert VCF to pg\_snp and gd\_snp](https://help.galaxyproject.org/t/convert-vcf-to-pg-snp-and-gd-snp/9220)
**Author:** [@mnowicki](https://help.galaxyproject.org/u/mnowicki)\ **Replies:** 4\ **Last updated:** [April 13, 2023, 12:38am UTC](https://help.galaxyproject.org/t/convert-vcf-to-pg-snp-and-gd-snp/9220 "2023-04-13T00:38:43Z")
Hi, When using “VCF to pg\_snp” (with idea to reformat later to gd\_snp), Galaxy fails. The tool does not accept that some alleles have alternatives: An error occurred with this dataset: format interval database ? bad … --- ## [gatk picard index builder error](https://help.galaxyproject.org/t/gatk-picard-index-builder-error/9200)
**Author:** [@apolitics](https://help.galaxyproject.org/u/apolitics)\ **Replies:** 3\ **Last updated:** [February 10, 2023, 8:42pm UTC](https://help.galaxyproject.org/t/gatk-picard-index-builder-error/9200 "2023-02-10T20:42:53Z")
An error occurred while running the tool data manager gatk picard index builder (the only version of the manager 0.0.1) - I was just trying to build the indexes for the GATK tools, and I didn’t succed (galaxy 22.05 w… [Next page](https://help.galaxyproject.org/tag/tool-deprecated/163.md?match_all_tags=true&page=1&tags%5B%5D=tool-deprecated)