Hello, I have built the SnpEff4.3 database for Salmo salar's chromosome 25 from Genbank and I have analyzed with SnpEff eff: annotate variants (Galaxy Version 4.3+T.galaxy2).I have obtained results for Chromosome 25. Now, I need to keep at the analyzing for the other chromosomes. For example, I did for Chromosome 8 and 9 exactly the same way but It didn't build SnpEff4.3 databases for them. But I built for chromosome 28 also. I need for all chromosomes. Please help me to solve this problem. I am using usegalaxy The error message as follow:
Fatal error: Exit code 255 (Error) Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/019/880/19880994/_job_tmp -Xmx7g -Xms256m 00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani 00:00:00 Command: 'build' 00:00:00 Building database for 'ssa08' 00:00:00 Reading configuration file 'snpEff.config'. Genome: 'ssa08' 00:00:00 Reading config file: /galaxy-repl/main/jobdir/019/880/19880994/working/snpEff.config 00:00:00 Reading config file: /cvmfs/main.galaxyproject.org/deps/_conda/pkgs/snpeff-4.3.1t-0/share/snpeff-4.3.1t-0/snpEff.config 00:00:01 done Chromosome: 'ssa08' length: 26434011 java.lang.RuntimeException: Transcript 'NM_001140227.1' is already in Gene 'GeneID:100195198' at org.snpeff.interval.IntervalAndSubIntervals.add(IntervalAndSubIntervals.java:44) at org.snpeff.snpEffect.factory.SnpEffPredictorFactory.add(SnpEffPredictorFactory.java:133) at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.addMrna(SnpEffPredictorFactoryFeatures.java:183) at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.addFeatures(SnpEffPredictorFactoryFeatures.java:134) at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:330) at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:369) at org.snpeff.SnpEff.run(SnpEff.java:1183) at org.snpeff.SnpEff.main(SnpEff.java:162) java.lang.RuntimeException: Error reading file '/galaxy-repl/main/jobdir/019/880/19880994/dataset_25853021_files/ssa08/genes.gbk' java.lang.RuntimeException: Transcript 'NM_001140227.1' is already in Gene 'GeneID:100195198' at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:344) at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:369) at org.snpeff.SnpEff.run(SnpEff.java:1183) at org.snpeff.SnpEff.main(SnpEff.java:162) 00:00:08 Logging 00:00:09 Checking for updates... 00:00:10 Done.
