# SnpEff build: Create Manihot esuclenta database **URL:** \ **Category:** Uncategorized\ **Tags:** tool-help, snpeff, snpeff\_build\_gb\ **Created:** [April 24, 2024, 5:46pm UTC](https://help.galaxyproject.org/t/snpeff-build-create-manihot-esuclenta-database/12302 "2024-04-24T17:46:20Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Emili\_Ishikawa\_Garci](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/emili_ishikawa_garci/32/5493_2.png) [@Emili\_Ishikawa\_Garci](https://help.galaxyproject.org/u/Emili_Ishikawa_Garci)\ **Post date:** [April 24, 2024, 5:46pm UTC](https://help.galaxyproject.org/t/snpeff-build-create-manihot-esuclenta-database/12302/1 "2024-04-24T17:46:20Z")
Hi, I need to identify if some SNPs obtained through GBS are synonymous or non-synonymous mutations and what their effect is on the sequences. To do this, I am trying to create a database for Manihot esculenta V8.1, using as input the .fa genome and the genes in .gtf format. However, the process throws an error after three days of running. The error image it throws is this: slurmstepd: error: \*\*\* JOB 1771297 ON js2-xl8 CANCELLED AT 2024-04-24T15:41:31 DUE TO TIME LIMIT \* Could someone guide me with this error, thank you very much ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 24, 2024, 7:02pm UTC](https://help.galaxyproject.org/t/snpeff-build-create-manihot-esuclenta-database/12302/2 "2024-04-24T19:02:27Z")
Hi @Emili_Ishikawa_Garci Are you working at [UseGalaxy.eu](http://UseGalaxy.eu)? I’m asking since the resource allocation should be enough at that server. Would you like to share a history that contains your input reference fasta and reference annotation, and the failed run? We could review for potential problems and provide feedback. How to share your work: - [Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/docs?topic=42) - [How to get faster help with your question](https://help.galaxyproject.org/docs?topic=11469) You might want to first review prior help, too. Remember that technical errors in the input files can lead to “false” resource errors. The solution is to fix the data formats and rerun. But we can help with format problems here if you get stuck. This is one prior Q&A, and more can be found here #snpeff > [@Subject: Urgent Assistance Needed with SnpEff Custom Database Creation](https://help.galaxyproject.org/t/subject-urgent-assistance-needed-with-snpeff-custom-database-creation/11504/2): > > We don’t have a specific tutorial for this since how the tool works in Galaxy is the same as for the command-line version. That means the author resources are the help. Technically, Galaxy creates a sort of mini-database with the output but those are not exposed to users. > > Some tips: > > 1. Use properly formatted reference data as the source > 2. Review the help on the tool form, and the link outs to the author resources > 3. Be careful about how you are adding labels on the tool form. The database name should be all oneWord and not starting with a number. If you run the tool several times, use a _distinct database name_ for each run to avoid clashes. I tend to just number them as I change my mind about the parameters: species1, species2, speciesN. Let’s start there 🙂 ---
**Author:** ![Emili\_Ishikawa\_Garci](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/emili_ishikawa_garci/32/5493_2.png) [@Emili\_Ishikawa\_Garci](https://help.galaxyproject.org/u/Emili_Ishikawa_Garci)\ **Post date:** [June 27, 2024, 10:51pm UTC](https://help.galaxyproject.org/t/snpeff-build-create-manihot-esuclenta-database/12302/3 "2024-06-27T22:51:36Z")
Dear Jennaj, thank you for you time and attention. You were right, the problem arose because I had the wrong input format. I corrected it and the tool ran perfectly. However, in the statistics table I get some “warnings” and some “errors” of which I cannot explore any details. Do you have any idea what I can do? ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [June 29, 2024, 8:28am UTC](https://help.galaxyproject.org/t/snpeff-build-create-manihot-esuclenta-database/12302/4 "2024-06-29T08:28:46Z")
Hi @Emili_Ishikawa_Garci warnings and errors are a common issue with custom-built SnpEff genome files indeed and it is a good idea to explore and try to understand them in detail. You can find both warnings and errors in the INFO field of specific variants in the annotated VCF. Their meanings are explained here: [Frequently Asked Questions - SnpEff & SnpSift](http://pcingola.github.io/SnpEff/snpeff/faq/)