GenerateFastaFiles fails

[intikhab]

Dear BG7,

Your BG7 setup looks quite interesting and I was testing it on one of our genomes. Manually going through different steps I notice that only GenerateFastaFiles code fails all others run correctly.

I get the following error:

Could not find the main class: com.era7.bioinfo.annotation.GenerateFastaFiles. Program will exit.

If it would have been a classpath problem, other tools in BG7 may also complain but it is only GenerateFastaFiles.

Any Help Please?

Intikhab

PS. Following is a test for different tools in BG7. I have downloaded the master branch from github last week.

alamis:BG7-master$ java -jar jars/PredictGenes.jar 
This program expects six parameters: 
1. BlastOutput XML filename 
2. Contigs FNA filename 
3. Output results XML filename 
4. Maximum gene length (integer)
5. Flag (boolean) indicating if this genome corresponds to a virus (true/false)
6. Dif span (integer)

alamis:BG7-master$ java -jar jars/GenerateFastaFiles.jar 
Exception in thread "main" java.lang.NoClassDefFoundError: com/era7/lib/bioinfo/bioinfoutil/Executable
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
    at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Caused by: java.lang.ClassNotFoundException: com.era7.lib.bioinfo.bioinfoutil.Executable
    at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
    ... 12 more
Could not find the main class: com.era7.bioinfo.annotation.GenerateFastaFiles. Program will exit.
alamis:BG7-master$ java -jar jars/GenerateGffFile.jar 
This program expects two parameters: 
1. Input predicted genes XML filename 
2. Output GFF filename

[pablopareja]

Hi Intikhab,

Thanks for opening this issue, I just realized that the /jar folder of the master branch had a lot of deprecated old jars that shouldn't be used anymore (things were updated in the develop branch but I forgot to do so in the master one)

The right way to execute any program from BG7's pipeline is by means of the jar called
BG7.jar together with an executions XML file where you can specify the sequence of programs that should be run, (in any case I got rid of the old jar files so that this cannot happen again to someone else).
You can find a template of the executions.xml file here: https://github.com/bg7/BG7/blob/master/executionsTemplate.xml

Hope this helps.