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
Are you working at 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.
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
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?
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
