snpEff mouse annotation failed because of computer resource limitation?

Question

[zengtony743]

I set the amount of memory in java virtual machine from 4G to 75G... it just failed.

$ java -Xmx75G -jar path/snpEff/4.11/snpEff.jar GRCm38.71 myfile.vcf > myfile.ann.vcf &


$ java.lang.RuntimeException: java.lang.RuntimeException: Cannot create directory '/hpf/tools/centos6/snpEff/source/data/GRCm38.71'
    at ca.mcgill.mcb.pcingola.util.Download.unzip(Download.java:255)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:32)
    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:920)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadDb(SnpEff.java:320)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:938)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:921)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:883)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:128)
Caused by: java.lang.RuntimeException: Cannot create directory '/hpf/tools/centos6/snpEff/source/data/GRCm38.71'
    at ca.mcgill.mcb.pcingola.util.Download.unzip(Download.java:223)
    ... 9 more
java.lang.RuntimeException: Genome download failed!
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadDb(SnpEff.java:321)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:938)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:921)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:883)
    at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:128)

[1]+  Exit 255                java -Xmx75G -jar path//snpEff/4.11/snpEff.jar GRCm38.71 myfile.vcf > myfile.ann.vcf

[GenoMax]

Appears you do not have permissions to create a directory in that path.

Cannot create directory '/hpf/tools/centos6/snpEff/source/data/GRCm38.71'

[zengtony743]

Thanks genomax2 . That is weird. I use a snpEff package via a public open resource from my working place. Now I have to download it and run it under my account seeing how it goes

[WouterDeCoster]

You may have to change the data.dir if you can't write to the location that was specified, see http://snpeff.sourceforge.net/download.html