After execution of the job for processing of the normalized with VT Tools Pilon`s VCF file we have:
WARNING: All frames are zero! This seems rather odd, please check that 'frame' information in your 'genes' file is accurate. java.lang.RuntimeException: Most Exons do not have sequences! at ca.mcgill.mcb.pcingola.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:129) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.createSnpEffPredictor(SnpEffCmdBuild.java:104) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:284) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:734) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:123) java.lang.RuntimeException: Error reading file '/home/galaxy/galaxy/database/jobs_directory/000/105/working/17266/./data/myspecies/genes.gff' java.lang.RuntimeException: Most Exons do not have sequences! at ca.mcgill.mcb.pcingola.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:133) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.createSnpEffPredictor(SnpEffCmdBuild.java:104) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:284) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:734) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:123)
NEW VERSION! There is a new SnpEff version available: Version : 4.3K Release date : 2017-03-13 Download URL : http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip
00:00:00.000 ERROR while connecting to https://snpeff-data.galaxyproject.org/databases/v4_0/snpEff_v4_0_myspecies.zip java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at ca.mcgill.mcb.pcingola.util.Download.download(Download.java:147) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:31) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:85) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:71) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:768) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadDb(SnpEff.java:299) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:683) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:663) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:734) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:123) Caused by: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at ca.mcgill.mcb.pcingola.util.Download.download(Download.java:96) ... 9 more java.lang.RuntimeException: Genome download failed! at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadDb(SnpEff.java:300) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:683) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:663) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:734) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:123)
NEW VERSION! There is a new SnpEff version available: Version : 4.3K Release date : 2017-03-13 Download URL : http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip
How to fix this error to produce a correct SNPEff annotation report?