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  • 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

  • #2
    Do you have snpEff.config in /GenoStorage/Software/snpEff_2_0_5d/ ?

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

    Comment


    • #3
      I have snpEff in one place and snpEff.config in another.

      That is possible?

      Comment


      • #4
        Anything's possible in a possible world

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

        Comment


        • #5
          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 ?

          Comment


          • #6
            Yes try it out

            Comment


            • #7
              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

              Comment


              • #8
                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).

                Comment


                • #9
                  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

                  Comment


                  • #10
                    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]

                    Comment


                    • #11
                      I don't have permission to do that, but I already asked for it.

                      Now I have to wait to see if it worked

                      Comment


                      • #12
                        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

                        Comment


                        • #13
                          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

                          Comment


                          • #14
                            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

                            Comment


                            • #15
                              What about 'GRCh37.65', as mentioned in the 'Latest' column on this page:

                              Comment

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