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Old 02-20-2012, 07:56 AM   #1
fc35802
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Question snpEff error

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
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Old 02-20-2012, 10:47 AM   #2
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Do you have snpEff.config in /GenoStorage/Software/snpEff_2_0_5d/ ?

If it's elsewhere you can specify that with -c
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Old 02-20-2012, 10:53 AM   #3
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I have snpEff in one place and snpEff.config in another.

That is possible?
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Old 02-20-2012, 11:09 AM   #4
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Anything's possible in a possible world

If I remember correctly, with the default install, it should be in the same directory
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Old 02-20-2012, 11:16 AM   #5
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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 ?
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Old 02-20-2012, 01:01 PM   #6
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Yes try it out
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Old 02-21-2012, 12:06 AM   #7
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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
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Old 02-21-2012, 12:30 AM   #8
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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:
Code:
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).
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Old 02-21-2012, 12:40 AM   #9
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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
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Old 02-21-2012, 12:50 AM   #10
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Quote:
Originally Posted by fc35802 View Post
I think it didn't fail

Code:
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:

Code:
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]
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Old 02-21-2012, 01:13 AM   #11
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I don't have permission to do that, but I already asked for it.

Now I have to wait to see if it worked
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Old 02-21-2012, 07:38 AM   #12
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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
[[email protected] 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
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Old 02-21-2012, 07:43 AM   #13
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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:
Code:
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
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Old 02-21-2012, 07:46 AM   #14
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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
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Old 02-21-2012, 07:51 AM   #15
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What about 'GRCh37.65', as mentioned in the 'Latest' column on this page:

http://snpeff.sourceforge.net/download.html
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Old 02-21-2012, 07:54 AM   #16
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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
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Old 02-21-2012, 07:59 AM   #17
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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.ht...guration_file?
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Old 02-21-2012, 08:08 AM   #18
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I tried to do that in the snpEff.config file but i won't let me save
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Old 02-21-2012, 08:23 AM   #19
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Quote:
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):

Code:
chown pcadmin:geneusers <location>/snpEff.config
chmod ug+w <location>/snpEff.config
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Old 02-22-2012, 12:31 AM   #20
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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
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