Frequently Asked Questions

1. I am getting the following error when running MetaTissueInputGenerator.jar

Exception in thread "main" java.lang.UnsupportedClassVersionError:
CreateInputForMetaTissue : Unsupported major.minor version 51.0

Please install the latest Java (1.7 or higher) from the Oracle and try again. Or please download jar files compiled with Java 1.6 version (available in download section).

2. I am getting the following error when running MetaTissueInputGenerator.jar

Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.simontuffs.onejar.Boot.run(Boot.java:342)
at com.simontuffs.onejar.Boot.main(Boot.java:168)
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -1
at java.lang.String.substring(Unknown Source)
at CreateInputForMetaTissue.readProbeInformation(CreateInputForMetaTissue.java:164)
at CreateInputForMetaTissue.execute(CreateInputForMetaTissue.java:652)
at CreateInputForMetaTissue.main(CreateInputForMetaTissue.java:808)
... 6 more

This error means that chromosome information in probe information file is incorrect. Please note that chromosome information must start with "chr" For example, for chromosome 3, it must be "chr3".

3. I am getting standard error of some SNP equal to 0, which aborts Metasoft bash script.

Please make sure those SNPs are polymorphic (MAF > 0%) and do not contain many missing genotypes. Please perform the standard GWAS QC (MAF, HWE, missingness) on SNPs before running Meta-Tissue.

4. I am getting segmentation fault when running MetaTissueMM in step 3.

MetaTissueMM runs only in Linux (tested in CentOS). If you encounter a seg fault error when running MetaTissueMM, please try this version of MetaTissueMM. If it still does not work, please try to run it in a different linux machine. Or try this version if you encounter seg fault or tissue-by-tissue results give very different results from linear regression in R.