[fc35802]

It doesn't work either

java -Xmx4G -jar /GenoStorage/Software/snpEff_2_0_5d/snpEff.jar eff -c /GenoStorage/Software/snpEff_2_0_5d/snpEff.config -v -onlyCoding true -i vcf -o txt GRCh37.65 varSample02187ATESTE.flt.vcf > snpEff_sample02187A.txt
00:00:00.000 Reading configuration file '/GenoStorage/Software/snpEff_2_0_5d/snpEff.config'
00:00:00.225 done
00:00:00.225 Reading database for genome 'GRCh37.65' (this might take a while)
java.lang.RuntimeException: java.io.FileNotFoundException: /GenoStorage/Software/snpEff_2_0_5d/./data/GRCh37.65/snpEffectPredictor.bin (No such file or directory)
at ca.mcgill.mcb.pcingola.Gpr.readFileSerializedGz(Gpr.java:426)
at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:48)
at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:101)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:536)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:244)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:72)
Caused by: java.io.FileNotFoundException: /GenoStorage/Software/snpEff_2_0_5d/./data/GRCh37.65/snpEffectPredictor.bin (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:137)
at java.io.FileInputStream.<init>(FileInputStream.java:96)
at ca.mcgill.mcb.pcingola.Gpr.readFileSerializedGz(Gpr.java:421)
... 5 more
00:00:00.235 Finishing up

[gringer]

That's a different error. You now have another file not found error because it's looking for '/GenoStorage/Software/snpEff_2_0_5d/./data/GRCh37.65/snpEffectPredictor.bin' rather than '/GenoStorage/BasesDados/GRCh37.65/snpEffectPredictor.bin'. You may need to change the data_dir parameter in the config file, because it's looking in the same directory that you mentioned your config file was in.

http://snpeff.sourceforge.net/faq.html#Can_you_explain_the_configuration_file?

[fc35802]

I tried to do that in the snpEff.config file but i won't let me save

[gringer]

I tried to do that in the snpEff.config file but i won't let me save

This is the config file that was owned by root that you enabled read access to? If you want to modify that, you'll need to enable write access globally as well, which means that anyone else using your computer system can modify that file (i.e. a bad idea).

You could also set the ownership of that config file to your user name, which would mean only you (and root) could modify it, or possibly match the ownership of the data directory, then set group permissions for write access (so people in that group can modify the config file):

chown pcadmin:geneusers <location>/snpEff.config
chmod ug+w <location>/snpEff.config

[fc35802]

It worked

Thanks a lot for your help

java -Xmx4G -jar /GenoStorage/Software/snpEff_2_0_5d/snpEff.jar eff -c /GenoStorage/Software/snpEff_2_0_5d/snpEff.config -v -onlyCoding true -i vcf -o txt hg19 varSample02187ATESTE.flt.vcf > snpEff_sample02187A.txt
00:00:00.000 Reading configuration file '/GenoStorage/Software/snpEff_2_0_5d/snpEff.config'
00:00:00.226 done
00:00:00.226 Reading database for genome 'hg19' (this might take a while)
00:00:13.202 done
00:00:13.203 Building interval forest
00:00:27.282 done.
00:00:27.282 Predicting variants
00:00:33.278 Creating summary file: snpEff_summary.html
00:00:34.303 Creating genes file: snpEff_genes.txt
00:00:39.008 done.
00:00:39.010 Finishing up