Question: snpEff genome database build problem: no snpEffectorPredit
0
gravatar for HannahT
2.4 years ago by
HannahT0
HannahT0 wrote:

Hello,

I am using snpEff to build a genome database. When I execute the following command:

java -jar snpEff.jar build -gff3 -v Sorghum

it appears that the program is running.

This information begins scrolling through the screen:

00:00:00    SnpEff version SnpEff 4.3p (build 2017-06-06 09:55), by Pablo Cingolani
00:00:00    Command: 'build'
00:00:00    Building database for 'Sorghum'
00:00:00    Reading configuration file 'snpEff.config'. Genome: 'Sorghum'
00:00:00    Reading config file: /home/.conda/pkgs/snpeff-4.3.1p-1/share/snpeff-4.3.1p-1/snpEff.config
00:00:01    done
Reading GFF3 data file  : '/home/.conda/pkgs/snpeff-4.3.1p-1/share/snpeff-4.3.1p-1/data/Sorghum/genes.gff'

And then it continues adding genomic sequences.

I do get some of the following warning messages:
WARNING: Cannot find last exonic position before 1748688 for transcript 'Sobic.002G018901.1.v3.2'
WARNING: Cannot find last exonic position before 42880109 for transcript 'Sobic.003G175350.1.v3.2'
WARNING: Cannot find first exonic position after 117023 for transcript 'Sobic.002G000350.1.v3.2'

And towards the end of reading sequences and adding sequences I get the following information:

java.lang.RuntimeException: Error reading file '/home/.conda/pkgs/snpeff-4.3.1p-1/share/snpeff-4.3.1p-1/data/Sorghum/genes.gff'
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:353)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.createSnpEffPredictor(SnpEffCmdBuild.java:118)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:362)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:30    Logging
00:00:31    Checking for updates...
00:00:32    Done.

Finally, how I think I detected the problem is that the 'snpEffectorPredictor.bin' is never created which is needed for downstream applications.

Is anyone familiar with this problem? Am I not completing the build? Or is it failing. I have a hard time believing it is my gff file since the initial start of the program seems to be working with no errors.

Thank you Hannah

snp • 1.6k views
ADD COMMENTlink modified 2.4 years ago by Pierre Lindenbaum124k • written 2.4 years ago by HannahT0

Not a direct solution but sorghum genome is supported.

java -jar snpEff.jar download Sorghum_bicolor

downloaded the bin in the data directory. Is there a specific reason that you want to build it yourself ?

ADD REPLYlink written 2.4 years ago by microfuge1.5k

My vcf file is based on the most recent Sorghum genome assembly while older versions are supported in snpeff. I think at this point I am going to redo the analysis using an older version of the genome.

Thanks

ADD REPLYlink written 2.4 years ago by HannahT0
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