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