DiscoverySNPCallerPlugin error

[Douglas Crawford]

Good Morning,
  I am using SNP discovery using the most recent version of Tassel4 on a dataset I have succesfully run on Tassel3 (TagsToSNPByAlignmentPlugin). 
When I run -DiscoverySNPCallerPlugin using either "pivotedTBT.h5" or  " myMastertag.tbt.byte"  the process hangs up at the same place 
(full logfile is attached)

my command:
~/Programs/tassel4/run_pipeline.pl -fork1 -DiscoverySNPCallerPlugin -i ~/Projects/4Acer/mergedTBT/myMastertag.tbt.byte -y -m ~/Projects/4Acer/topm/myMasterTags.topm -mUpd ~/Projects/4Acer/topm/myMasterTagsWithVariants.topm -o ~/Projects/4Acer/hapmap/raw/myGBSGenos_chr+.hmp.txt -mnMAF 0.01 -mnMAC 100000 -ref ~/Projects/4Acer/Acropora_genome/adi_v1.0.scaffold_2.fa -sC 1 -eC 4765 -endPlugin -runfork1

PART OF THE ERROR   is  listed below  (see attached for complete log)
Exception in thread "Thread-0" java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation
    at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358)
    at org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88)
    at org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118)
    at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86)
    at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:69)
    at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71)
    at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342)
    at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112)
    at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112)
    at org.biojava3.alignment.FractionalIdentityScorer.getMaxScore(FractionalIdentityScorer.java:92)
    at org.biojava3.alignment.template.AbstractScorer.getDistance(AbstractScorer.java:40)
    at org.biojava3.alignment.template.AbstractScorer.getDistance(AbstractScorer.java:35)
    at org.biojava3.alignment.GuideTree.<init>(GuideTree.java:80)
    at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)
    at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:514)
    at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:309)
    at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.addSitesToMutableAlignment(DiscoverySNPCallerPlugin.java:519)
    at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.runTagsToSNPByAlignment(DiscoverySNPCallerPlugin.java:401)
    at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.performFunction(DiscoverySNPCallerPlugin.java:121)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
    at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

Any suggestion

[Douglas Crawford]

Hi,
   I re-ran Tassel4 pipeline with this dataset on an older mac and it worked fine.  
My current Mac (with the problem listed below) has OsX 10.9 (Mavericks) and I am hoping this is not the problem.
I will try re-running with bwa (instead of bowtie2) and see if this help.
Any other suggestions would be helpful.

dlc

[Terry Casstevens]

How did you install Tassel? Can you send the top of the log that
shows the Classpath? Could your installation be using a different
biojava than we distribute?

Cheers,

Terry

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[Douglas Crawford]

Good Morning,
     I think you want the information pasted below.  If not, please ask again.
2 things:   I update the Tassel4 on the old mac yesterday.
2nd: I am going to test the DiscoverySNPCallerPlugin by copying the files from the older mac and see if DiscoverySNPCallerPlugin works on these data.

My real concern is that with the new Xcode(5) there is a fault in my system. 

Thank you for your input.
DLC

On Monday, April 28, 2014 9:35:36 AM UTC-4, Douglas Crawford wrote:

[Douglas Crawford]

Sorry: 
The header information you wanted:

Douglass-MacBook-Pro-2:Projects admin$ ~/Programs/tassel4/run_pipeline.pl -fork1 -SAMConverterPlugin -i ~/Projects/4Acer/Ac_sam.sam -o ~/Projects/4Acer/topm/myMasterTags.topm -endPlugin -runfork1
/Users/admin/Programs/tassel4/lib/batik-awt-util.jar:/Users/admin/Programs/tassel4/lib/batik-css.jar:/Users/admin/Programs/tassel4/lib/batik-dom.jar:/Users/admin/Programs/tassel4/lib/batik-ext.jar:/Users/admin/Programs/tassel4/lib/batik-gui-util.jar:/Users/admin/Programs/tassel4/lib/batik-gvt.jar:/Users/admin/Programs/tassel4/lib/batik-parser.jar:/Users/admin/Programs/tassel4/lib/batik-svg-dom.jar:/Users/admin/Programs/tassel4/lib/batik-svggen.jar:/Users/admin/Programs/tassel4/lib/batik-util.jar:/Users/admin/Programs/tassel4/lib/batik-xml.jar:/Users/admin/Programs/tassel4/lib/biojava3-alignment-3.0.jar:/Users/admin/Programs/tassel4/lib/biojava3-core-3.0.jar:/Users/admin/Programs/tassel4/lib/biojava3-phylo-3.0.jar:/Users/admin/Programs/tassel4/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:/Users/admin/Programs/tassel4/lib/colt.jar:/Users/admin/Programs/tassel4/lib/commons-math-2.2.jar:/Users/admin/Programs/tassel4/lib/ejml-0.23.jar:/Users/admin/Programs/tassel4/lib/forester.jar:/Users/admin/Programs/tassel4/lib/geronimo-spec-activation-1.0.2-rc4.jar:/Users/admin/Programs/tassel4/lib/guava-14.0.1.jar:/Users/admin/Programs/tassel4/lib/itextpdf-5.1.0.jar:/Users/admin/Programs/tassel4/lib/jcommon-1.0.6.jar:/Users/admin/Programs/tassel4/lib/jfreechart-1.0.3.jar:/Users/admin/Programs/tassel4/lib/junit-4.1.jar:/Users/admin/Programs/tassel4/lib/LiuExt.jar:/Users/admin/Programs/tassel4/lib/log4j-1.2.13.jar:/Users/admin/Programs/tassel4/lib/mail-1.4.jar:/Users/admin/Programs/tassel4/lib/poi-3.0.1-FINAL-20070705.jar:/Users/admin/Programs/tassel4/lib/xercesImpl.jar:/Users/admin/Programs/tassel4/lib/xml.jar:/Users/admin/Programs/tassel4/lib/xmlParserAPIs.jar:/Users/admin/Programs/tassel4/sTASSEL.jar
Memory Settings: -Xms12G -Xmx14G

[Terry Casstevens]

This looks right. Did you download the standalone zip? Can you send
me the verbose listing on the biojava files?

ls -l biojava3*

What version of java are you using?

java -version

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[Douglas Crawford]

Hi Terry
  I believe this is what you want:
-rw-r--r--@ 1 admin  staff  111476 Dec 12 08:46 biojava3-alignment-3.0.jar
-rw-r--r--@ 1 admin  staff  271471 Dec 12 08:46 biojava3-core-3.0.jar
-rw-r--r--@ 1 admin  staff   59865 Dec 12 08:46 biojava3-phylo-3.0.jar

JAVA
java version "1.8.0"
Java(TM) SE Runtime Environment (build 1.8.0-b132)
Java HotSpot(TM) 64-Bit Server VM (build 25.0-b70, mixed mode)

by the by:  running bwa (vs bowtie) did not remove the problem.  I am about to move a folder with from the old mac and see if I can run discoverysnp on these files.

thanks
dlc

[Terry Casstevens]

This seems to have something to do with Java 8. When I run it under
Java 8, I get the same error.

> https://groups.google.com/d/msgid/tassel/e48522c5-4d1f-4f95-a793-dda721a355d9%40googlegroups.com.

[Douglas Crawford]

Hi Terry,
  Excellent.  Which Java should I be running? 
cheers
dlc

[Terry Casstevens]

Hi Douglas,

In theory, it should work with Java 8. But most folks are using Java
7 which is the lowest version that can be used with Tassel 4 and 5.

Cheers,

Terry

> https://groups.google.com/d/msgid/tassel/81b95fd0-7008-4519-97b8-319775c69f08%40googlegroups.com.

[Douglas Crawford]

Hi Terry,
    I am having a difficult time installing Java1.7 because I.8 exist.   I followed Oracle advice and deleted jdk.1.8----   
But after a reboot,  1.8 exist.

Any suggestion so I can get DiscoverySNPCaller to work?

dlc

example
/Library/Java/JavaVirtualMachines/jdkmajor.minor.macro[_update].jdk
For example, to uninstall 8u6:
% rm -rf jdk1.8.0_06.jdk

[Terry Casstevens]

Try this command to switch on MAC

export JAVA_HOME=`/usr/libexec/java_home -v 1.7`

> https://groups.google.com/d/msgid/tassel/82c7e5f3-5dd0-4048-a6fd-0aee3c63adeb%40googlegroups.com.

[Douglas Crawford]

Hi Terry,
   Thank you for all your time and efforts.   Unfortunately, I do not have version Java7 (new mac, newest Java 1.8 and the default Java1.6).
   Using your recommendation with 1.6 (not 1.7)
export JAVA_HOME=`/usr/libexec/java_home -v 1.6`

On Tuesday, April 29, 2014 3:57:17 PM UTC-4, Terry wrote:

Try this command to switch on MAC

export JAVA_HOME=`/usr/libexec/java_home -v 1.7`

I get a Java error  (see below ____ line_______).
reverting back to 1.8,  I get the original error that we have been discussing.

A little frustrated.

cheers
dlc

__________________line_________

Exception in thread "main" java.lang.UnsupportedClassVersionError: net/maizegenetics/pipeline/TasselPipeline : Unsupported major.minor version 51.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
    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)

[Terry Casstevens]

Tassel 4 and 5 require at least Java 7. That error means your Java is
to old to run Tassel.

> https://groups.google.com/d/msgid/tassel/f1d1644f-98dc-492e-a9c4-0ba3036f576f%40googlegroups.com.

[Douglas Crawford]

Hi Terry:

     So yes,  one Java(1.6) is too old

   The other (1.8) is too new

and there no way to install just right (Java1.7).

So is there any hope of a solution?

dlc

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--
Douglas L. Crawford
Marine Biology & Fisheries
Rosenstiel School of Marine & Atmospheric Sciences
4600 Rickenbacker Cswy
Miami, FL 33149
305-421-4121
http://crawford.rsmas.miami.edu/

[David Dayan]

Terry,
  Yes.  Java8 is too new.  My Java6 is too old and I cannot load Java7 because Java8 exist. 
I am wondering if I am sol and have to go back to my old mac?  2nd: I am wondering if Tassel pipeline will eventually work with Java8?

Thanks again.  I do appreciate the input.

cheers
dlc

[Terry Casstevens]

Hi Douglas,

Why can't you install Java 7. You can get it here.

http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html

Yes, we will likely move to Java 8 at the end of this year.

Best,

Terry

> https://groups.google.com/d/msgid/tassel/CAOS4FG3cbtJQn9dO3hxXtiCQd7dWmcC3QpUR_nKnbh2628mKtA%40mail.gmail.com.

[Edward S. Buckler]

TASSEL 5 should run under Java 8 ok. I run in practice mode in 8 all the
time.

--
Ed Buckler

>>>https://groups.google.com/d/msgid/tassel/81b95fd0-7008-4519-97b8-319775c
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[Douglas Crawford]

Hi Terry,

  Yes, I have it, but it will not install.  I get the error message :"newer version exist".  All attempts to   remove Java8 (Oracles suggestion (detail below)  have not worked-- I still cannot install Java7 (newer version still exist)

Oracle:  to remove Java8
Navigate to /Library/Java/JavaVirtualMachines and remove the directory whose name matches the following format:

/Library/Java/JavaVirtualMachines/jdkmajor.minor.macro[_update].jdk
For example, to uninstall 8u6:
% rm -rf jdk1.8.0_06.jdk

so

dlc

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[Douglas Crawford]

Hi guys,
    This is great!  That is, having insightful input by so many informed scientist.
To be sure I understand 
I am going to run Tassel pipeline with Tassel5.   Specifically, I am going to run the discoverySNP caller using Tassel5?

cheers
dlc

[Terry Casstevens]

Hi Ed,

Tassel 5 in general runs fine under Java 8. But something about the
biojava library used by DiscoverySNPCallerPlugin doesn't work with
Java 8.

Best,

Terry

> To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CF86BFBD.D617E%25esb33%40cornell.edu.

[Terry Casstevens]

Hi Douglas,

The issue you have with biojava and Java 8 will probably be the same
in Tassel 4 and 5 (we plan to fix that). Our objective is to use
Tassel 5 for everything. But I will let Jeff comment on current best
usage of GBS pipeline.

Best,

Terry

> https://groups.google.com/d/msgid/tassel/9f715d70-a5eb-46d3-8361-aff3a8f2d886%40googlegroups.com.

[Jeff Glaubitz]

Go ahead and try TASSEL5 and let us know if you notice any bugs or issues.

Jeff

--
Jeff Glaubitz
Project Manager
Genetic Architecture of Maize and Teosinte
National Science Foundation award 0820619
http://www.panzea.org
Institute for Genomic Diversity
Cornell University
175 Biotechnology Bldg
Ithaca, NY 14853
Phone: 607-255-1386
jcg...@cornell.edu

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[Douglas Crawford]

Hi,

    Unfortunately, Tassel 5 had the same problem (see below), although at a different position.

What I believe we think is that java8 has a problem with the pipeline although this is not apparent in the GUI Tassel (4 or 5). 

dlc

______  command ____
~/Programs/tassel5/run_pipeline.pl -fork1 -DiscoverySNPCallerPlugin -i ~/Projects/4Acer/tbt/pivotedTBT.h5 -m ~/Projects/4Acer/topm/myMasterTags.topm -mnF 0 -mnMAF 0.005 -mnMAC 10 -ref ~/Projects/4Acer/Acropora_genome/adi_v1.0.scaffold_2.fa -sC 1 -eC 4765 -o ~/Projects/4Acer/hapmap/raw/4Ac_Gtypes_ctg+.hmp.txt.gz -endPlugin -runfork1

___________   error

Exception in thread "Thread-1" java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation
    at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358)
    at org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88)

    at org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118)
    at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86)
    at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:69)

    at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71)
    at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342)
    at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112)
    at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112)
    at org.biojava3.alignment.FractionalIdentityScorer.getMaxScore(FractionalIdentityScorer.java:92)
    at org.biojava3.alignment.template.AbstractScorer.getDistance(AbstractScorer.java:40)

    at org.biojava3.alignment.template.AbstractScorer.getDistance(AbstractScorer.java:35)

    at org.biojava3.alignment.GuideTree.<init>(GuideTree.java:80)
    at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)

    at net.maizegenetics.dna.map.TagLocus.getVariableSites(TagLocus.java:501)
    at net.maizegenetics.dna.map.TagLocus.getSNPCallsQuant(TagLocus.java:297)
    at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.findSNPsInTagLocus(DiscoverySNPCallerPlugin.java:412)
    at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.discoverSNPsOnChromosome(DiscoverySNPCallerPlugin.java:360)
    at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.performFunction(DiscoverySNPCallerPlugin.java:105)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:227)
    at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

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[Edward S. Buckler]

Ugh, this must be a bug in the underlying biojava library.  The different position is likely from the multithreading that biojava uses, so it processes multiple alignments at the same time.

Only the GBS pipeline uses biojava extensively, which is why I haven’t seen it in code related to alignments.

This could be a hard bug to solve without getting biojava recompiled.

-Ed

  

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-- 
Ed Buckler
USDA-ARS Research Geneticist
Adj. Prof of Plant Breeding and Genetics

Institute for Genomic Diversity
Cornell University

159 Biotechnology Bldg
Ithaca, NY 14853-2703

Email:  es...@cornell.edu
Voice: (607) 255-4520
Fax: (607) 255-6249

Homepage: http://www.maizegenetics.net/

[Douglas Crawford]

Well at least you know there is a bug with Java8 and the GBS pipeline. 

cheers
dlc

&g

...

[Douglas Crawford]

One more observation:

   I ran UNEAK on this Mac with Java8.   Thus, the UNEAK pipeline worked, but the standard Tassel4 Pipeline does not.

dlc

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/1526E650-52DF-446B-94D8-C225E1D5C9AD%40cornell.edu.

For more options, visit https://groups.google.com/d/optout.

[Douglas Crawford]

Hi,
   One more thing:   the problem with Java8 and Tassel pipeline (inability to run DiscoverySNP) did NOT affect UNEAK SNP caller.

cheers
dlc

On Monday, April 28, 2014 9:35:36 AM UTC-4, Douglas Crawford wrote:

Good Morning,
  I am using SNP discovery using the most recent version of Tassel4 on a dataset I have succesfully run on Tassel3 (TagsToSNPByAlignmentPlugin). 
When I run -DiscoverySNPCallerPlugin using either "pivotedTBT.h5" or  " myMastertag.tbt.byte"  the process hangs up at the same place 
(full logfile is attached)

my command:
~/Programs/tassel4/run_pipeline.pl -fork1 -DiscoverySNPCallerPlugin -i ~/Projects/4Acer/mergedTBT/myMastertag.tbt.byte -y -m ~/Projects/4Acer/topm/myMasterTags.topm -mUpd ~/Projects/4Acer/topm/myMasterTagsWithVariants.topm -o ~/Projects/4Acer/hapmap/raw/myGBSGenos_chr+.hmp.txt -mnMAF 0.01 -mnMAC 100000 -ref ~/Projects/4Acer/Acropora_genome/adi_v1.0.scaffold_2.fa -sC 1 -eC 4765 -endPlugin -runfork1

PART OF THE ERROR   is  listed below  (see attached for complete log)
Exception in thread "Thread-0" java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation

    at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358)
    at org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88)
    at org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118)
    at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86)
    at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:69)
    at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71)
    at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342)
    at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112)
    at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112)
    at org.biojava3.alignment.FractionalIdentityScorer.getMaxScore(FractionalIdentityScorer.java:92)
    at org.biojava3.alignment.template.AbstractScorer.getDistance(AbstractScorer.java:40)
    at org.biojava3.alignment.template.AbstractScorer.getDistance(AbstractScorer.java:35)
    at org.biojava3.alignment.GuideTree.<init>(GuideTree.java:80)
    at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176)

    at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:514)
    at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:309)
    at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.addSitesToMutableAlignment(DiscoverySNPCallerPlugin.java:519)

[Xuewen Wang]

Dear all,

I am using Tassel 3 command pipeline to analyze the GBS data to get SNP from a population, and have the similar problem on "TagsToSNPByAlignmentPlugin". This plugin of the pipeline is not stable.
The log says parameters are wrong and -i option file is not found. Actually the file is there. I tested this using command as below:

ls -l mergedTBT/myStudyp1.tbt.byte
#the output shows the file in there. pasted in the following line.
rw-r--r-- 1 wangxuewen users 525220792 2014-05-01 00:18 mergedTBT/myStudyp1.tbt.byte

I also paste the full log file containing the details below. Has anyone have good suggestion on how to resolve the problem? Does anyone know how to use the graphic interface to do GBS SNP analyzing?
Thanks.
Xuewen Wang

below is the log information:
The following is the error message : [main] ERROR net.maizegenetics.pipeline.

TasselPipeline - java.lang.IllegalArgumentException: Can't find the TagsByTaxa input file (-i option: mergedTBT/myStudyp1.tbt.byte).

Xuewen

detailed full message:


Memory Settings: -Xms512m -Xmx12G
Tassel Pipeline Arguments: -fork1 -TagsToSNPByAlignmentPlugin -y -i mergedTBT/myStudyp1.tbt.byte -m topm/myMasterTags.topm -mUpd topm/myMasterTagsWithVariants.

topm -o h
apmap/raw/myGBSGenos_chr+.hmp.txt -mnF 0.8 -p myPedigreeFile.ped -ref refseq -mnMAF 0.01 -mnMAC 100000 -sC 1 -eC 212441 -endPlugin -runfork1
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 3.0.164  Date: December 5, 2013
INFO -


The available options for the TagsToSNPByAlignmentPlugin are as follows:
-i       Input .tbt file
-y       Use byte-formatted TBT file (*.tbt.byte)
-m       TagsOnPhysicalMap file containing genomic position of tags
-mUpd    Update TagsOnPhysicalMap file with allele calls, saved to specified file
-o       Output HapMap file. Use a plus sign (+) as a wild card character in place of the chromosome number
             (e.g., ./hapmap/raw/myGBSGenos_chr+.hmp.txt)
-mxSites Maximum number of sites (SNPs) output per chromosome (default: 200000)
-mnF     Minimum F (inbreeding coefficient) (default: -2.0  = no filter)
-p       Pedigree file containing full sample names (or expected names after merging) & expected inbreeding
         coefficient (F) for each.  Only taxa with expected F >= mnF used to calculate F = 1-Ho/He.
         (default: use ALL taxa to calculate F)
-mnMAF   Minimum minor allele frequency (default: 0.01)
-mnMAC   Minimum minor allele count (default: 10)
-mnLCov  Minimum locus coverage (proportion of Taxa with a genotype) (default: 0.1)
-errRate Average sequencing error rate per base (used to decide between heterozygous and homozygous calls) (default: 0.01)
-ref     Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included
         when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site
         is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon).
         DEFAULT: Don't use reference genome.
-inclRare  Include the rare alleles at site (3 or 4th states) (default: false)
-inclGaps  Include sites where major or minor allele is a GAP (default: false)

-sC       Start chromosome
-eC       End chromosome



[main] INFO net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin -


The available options for the TagsToSNPByAlignmentPlugin are as follows:
-i       Input .tbt file
-y       Use byte-formatted TBT file (*.tbt.byte)
-m       TagsOnPhysicalMap file containing genomic position of tags
-mUpd    Update TagsOnPhysicalMap file with allele calls, saved to specified file
-o       Output HapMap file. Use a plus sign (+) as a wild card character in place of the chromosome number
             (e.g., ./hapmap/raw/myGBSGenos_chr+.hmp.txt)
-mxSites Maximum number of sites (SNPs) output per chromosome (default: 200000)
-mnF     Minimum F (inbreeding coefficient) (default: -2.0  = no filter)
-p       Pedigree file containing full sample names (or expected names after merging) & expected inbreeding
         coefficient (F) for each.  Only taxa with expected F >= mnF used to calculate F = 1-Ho/He.
         (default: use ALL taxa to calculate F)
-mnMAF   Minimum minor allele frequency (default: 0.01)
-mnMAC   Minimum minor allele count (default: 10)
-mnLCov  Minimum locus coverage (proportion of Taxa with a genotype) (default: 0.1)
-errRate Average sequencing error rate per base (used to decide between heterozygous and homozygous calls) (default: 0.01)
-ref     Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included
         when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site
         is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon).
         DEFAULT: Don't use reference genome.
-inclRare  Include the rare alleles at site (3 or 4th states) (default: false)
-inclGaps  Include sites where major or minor allele is a GAP (default: false)
-callBiSNPsWGap  Include sites where the third allele is a GAP (default: false)
-sC       Start chromosome
-eC       End chromosome



[main] ERROR net.maizegenetics.pipeline.TasselPipeline - java.lang.IllegalArgumentException: Can't find the TagsByTaxa input file (-i option: mergedTBT/myStudyp1.tbt.by
te).
java.lang.IllegalArgumentException: TasselPipeline: parseArgs: Unknown parameter: -TagsToSNPByAlignmentPlugin
        at net.maizegenetics.pipeline.TasselPipeline.parseArgs(TasselPipeline.java:1233)
        at net.maizegenetics.pipeline.TasselPipeline.<init>(TasselPipeline.java:121)
        at net.maizegenetics.pipeline.TasselPipeline.main(TasselPipeline.java:161)