snpEff error

[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

[mehc]

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

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

[fc35802]

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

That is possible?

[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 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]

Yes try it out

[fc35802]

I tried, but it didin't work

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 /GenoStorage/BasesDados/GRCh37.64 varSample02187ATESTE.flt.vcf > snpEff_sample02187A.txt
00:00:00.000 Reading configuration file '/GenoStorage/Software/snpEff_2_0_5d/snpEff.config'
java.lang.RuntimeException: Cannot find config file '/GenoStorage/Software/snpEff_2_0_5d/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)
00:00:00.008 Finishing up

[gringer]

The error mentions that java is unable to find a file at that location. You can check to make sure the file doesn't exist with ls:

ls '/GenoStorage/Software/snpEff_2_0_5d/snpEff.config'

If ls fails, then the Java command will also fail. Check the capitalisation of names, and make sure that your 'GenoStorage' directory is actually based off the root of the file system (which seems like a strange place to put it).

[fc35802]

I think it didn't fail

ls -lah '/GenoStorage/Software/snpEff_2_0_5d/snpEff.config'
-rw------- 1 root root 45K Jan 20 02:10 /GenoStorage/Software/snpEff_2_0_5d/snpEff.config

[gringer]

I think it didn't fail

ls -lah  '/GenoStorage/Software/snpEff_2_0_5d/snpEff.config'
-rw------- 1 root root 45K Jan 20 02:10 /GenoStorage/Software/snpEff_2_0_5d/snpEff.config

This file can only be read by root (oh, and thanks for making it long format so that I noticed this problem). If you're running Java as root, that's a bad idea, but I'm guessing based on the error that this is being run as a more normal user. You can change the file modes to permit reading with chmod:

chmod go+r '/GenoStorage/Software/snpEff_2_0_5d/snpEff.config'

[because this file is owned by root, you'll only be able to do that as root, or as a suitably privileged user]

[fc35802]

I don't have permission to do that, but I already asked for it.

Now I have to wait to see if it worked

[fc35802]

The problem of snpEff.config is solved, now I have another

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 /GenoStorage/BasesDados/GRCh37.65 varSample02187ATESTE.flt.vcf > snpEff_sample02187A.txt
00:00:00.000 Reading configuration file '/GenoStorage/Software/snpEff_2_0_5d/snpEff.config'
java.lang.RuntimeException: No such genome '/GenoStorage/BasesDados/GRCh37.65'
at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:48)
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)
00:00:00.226 Finishing up
[meusebio@IMMGene1 meusebio]$ ls -lah /GenoStorage/BasesDados/GRCh37.65/
total 67M
drwxr-xr-x 2 pcadmin geneusers 43 Feb 17 10:48 .
drwxrwx---. 6 pcadmin geneusers 84 Feb 17 10:53 ..
-rw-r--r-- 1 root root 67M Feb 17 10:48 snpEffectPredictor.bin

[gringer]

Disclaimer: I've never used snpEff, so can only guess at these things

Looking at the snpEff manual, it looks like you need the code name for the genome version, rather than a link to a particular file:

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 hg37

[fc35802]

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 hg37 varSample02187ATESTE.flt.vcf > snpEff_sample02187A.txt
00:00:00.000 Reading configuration file '/GenoStorage/Software/snpEff_2_0_5d/snpEff.config'
java.lang.RuntimeException: No such genome 'hg37'
at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:48)
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)
00:00:00.225 Finishing up

That would be nice, but didn't work

[gringer]

What about 'GRCh37.65', as mentioned in the 'Latest' column on this page:

http://snpeff.sourceforge.net/download.html