Error [pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null

[Dr Mathavan M]

Hello there,

I am working on GBS project, tassel is very new to me. I created the sTASSEL.jar file as per instruction. While running the command for the database creation it throws an error. I herewith attached the error message in debug mode. Kindly looking into the error massage

[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null

  at net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin.postProcessParameters(GBSSeqToTagDBPlugin.java:150)
        at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:107)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2017)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -

[Lynn Carol Johnson]

Is there a reason you are manually creating the jar file vs using the tassel-5-standalone which already has this compiled?

Please send the commands you are running and the full log file and I’ll take a look.

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[Dr Mathavan M]

Hello Lynn Johnson,

Thank you responding my queries, I manually added new enzyme HaeIII and MluCI and recompile it. Before  it was working fine but after adding the new enzyme it throws the errors!!!

Command used for re-complication

step 1 : git clone https://bitbucket.org/tasseladmin/tassel-5-source.git tassel5-src

Step 2: change the GBSEnzyme.java file

#Enzyme  edited code

/// EDITING HERE        
        } else if (enzyme.matches("(?i)haeiii|(?i)hae3")) {
            theEnzyme = "HaeIII"; // GG^CC
            initialCutSiteRemnant = new String[]{"CC"};
            likelyReadEnd = new String[]{"GGCC"};
            readEndCutSiteRemnantLength = 2;
        } else if (enzyme.matches("(?i)mluc[i1]")) {
            theEnzyme = "MluCI"; // "AATT
            initialCutSiteRemnant=new String[]{"AATT"};
            likelyReadEnd = new String[]{"AATT"};
            readEndCutSiteRemnantLength = 4;
/// END OF EDIT BLOCK

 replace the existing GBSEnzyme.java file to newly edited GBSEnzyme.java file

Step 3: recompiling using maven env

$ mvn clean package -Dmaven.test.skip=true -Dmaven.javadoc.skip=true

then a new sTASSEL.jar file created. I replaced the existing newly complied sTASSEL.jar file with default file

 step 4  : replace sTASSEL.jar file

step 5 : executing the command database file creation

./run_pipeline.pl  -debug -Xms514g -Xmx754g -fork1 -GBSSeqToTagDBPlugin -e MluCI -i . -db GBS_BM_MluCI.db -k fakebarcodes_key_MluCI.tsv -c 3 -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 100000000 -endPlugin -runfork1

[Lynn Carol Johnson]

Will you re-run, adding a file name to the debug command then send me the file?

./run_pipeline.pl ­debug [<filename>] … (rest of your command)

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[Lynn Carol Johnson]

Nevermind – I see you included a file in the original email.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/C4056C5D-EB7C-4CAB-AFB7-4A3C7C2E163A%40cornell.edu.

[Lynn Carol Johnson]

Ah … You are editing the wrong file.  The GBSEnzyme.java has been deprecated.  You need to edit the lib/enzymes.ini file.  I tested this manually.  I get the same error as you when the lib/enzymes.ini file has not been edited.

After editing the lib/enzymes.ini file and recompiling the code runs. 

I apologize for not having updated the wiki sooner, but you’ll now see an Enzymes section on this page:
https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline

 

The instructions for adding a new enzyme are these:

1.  Pull the tassel-5-source code

2.  Edit file lib/enzymes.ini

3.  compile and run

 

To the lib/enymes.ini file I added this code based on what you have below.  If you do the same, it should find your enzyme:

[HAEIII]

name = HaeIII

initialCutSiteRemnant = CC

likelyReadEnd = GGCC

readEndCutSiteRemnantLength = 2

 

[MLUCI]

name = MluCI

initialCutSiteRemnant = AATT

likelyReadEnd = AATT

readEndCutSiteRemnantLength = 4

Let me know if this fixes the problem

 

Thanks - Lynn

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/8bd65c2c-2633-4c05-8065-c5badbf709d1n%40googlegroups.com.