snpEff error

[fc35802]

I am not authorized to download to our server, so I have to ask someone to install all the programs.

So I use the command exactly as it is, but with -c and the path to snpEff.config ?

[mehc]

Anything's possible in a possible world

If I remember correctly, with the default install, it should be in the same directory

[fc35802]

I have snpEff in one place and snpEff.config in another.

That is possible?

[mehc]

Do you have snpEff.config in /GenoStorage/Software/snpEff_2_0_5d/ ?

If it's elsewhere you can specify that with -c

[fc35802]

Can you see the error in here?

Thanks in advance




java -Xmx4G -jar /GenoStorage/Software/snpEff_2_0_5d/snpEff.jar eff -v -onlyCoding true -i vcf -o txt /GenoStorage/BasesDados/GRCh37.64 varSample02187ATESTE.flt.vcf > snpEff_sample02187A.vcf
00:00:00.000 Reading configuration file 'snpEff.config'
java.lang.RuntimeException: Cannot find config file 'snpEff.config'
at ca.mcgill.mcb.pcingola.snpEffect.Config.read(Config.java:117)
at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:46)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:523)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:244)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:72)
00:00:00.007 Finishing up