Discover SNP Caller Plugin problem - BioJava
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Alex Twyford
Oct 1, 2014, 7:29:52 AM10/1/14
to tas...@googlegroups.com
Hi all,
I'm having a problem at the Discovery SNP Caller Plugin stage, which looks to relate to BioJava. It gets part way, gives an error message, then hangs. This problem may be the same as this one posted on another older thread that appears to have been unresolved:
I'm running the most recent version of Tassel (5.1) and Java 8. Any suggestions?
Thanks,
Alex
/mydata/GBS3/lib/LiuExt.jar:/mydata/GBS3/lib/batik-awt-util.jar:/mydata/GBS3/lib/batik-css.jar:/mydata/GBS3/lib/batik-dom.jar:/mydata/GBS3/lib/batik-ext.jar:/mydata/GBS3/lib/batik-gui-util.jar:/mydata/GBS3/lib/batik-gvt.jar:/mydata/GBS3/lib/batik-parser.jar:/mydata/GBS3/lib/batik-svg-dom.jar:/mydata/GBS3/lib/batik-svggen.jar:/mydata/GBS3/lib/batik-util.jar:/mydata/GBS3/lib/batik-xml.jar:/mydata/GBS3/lib/biojava3-alignment-3.0.jar:/mydata/GBS3/lib/biojava3-core-3.0.jar:/mydata/GBS3/lib/biojava3-phylo-3.0.jar:/mydata/GBS3/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:/mydata/GBS3/lib/colt.jar:/mydata/GBS3/lib/commons-math-2.2.jar:/mydata/GBS3/lib/ejml-0.23.jar:/mydata/GBS3/lib/forester.jar:/mydata/GBS3/lib/geronimo-spec-activation-1.0.2-rc4.jar:/mydata/GBS3/lib/guava-14.0.1.jar:/mydata/GBS3/lib/itextpdf-5.1.0.jar:/mydata/GBS3/lib/jcommon-1.0.6.jar:/mydata/GBS3/lib/jfreechart-1.0.3.jar:/mydata/GBS3/lib/json-simple-1.1.1.jar:/mydata/GBS3/lib/junit-4.10.jar:/mydata/GBS3/lib/log4j-1.2.13.jar:/mydata/GBS3/lib/mail-1.4.jar:/mydata/GBS3/lib/poi-3.0.1-FINAL-20070705.jar:/mydata/GBS3/lib/xercesImpl.jar:/mydata/GBS3/lib/xml.jar:/mydata/GBS3/lib/xmlParserAPIs.jar:/mydata/GBS3/sTASSEL.jar
Memory Settings: -Xms512m -Xmx10G
Tassel Pipeline Arguments: -debug -fork1 -DiscoverySNPCallerPlugin -i pivotedTBT/pivotedTBT.h5 -m topm/myMasterTags.topm -o hapmap/raw/myGBSGenos_chr+.hmp.txt -mnF -0.1 -mnMAF 0.02 -mnMAC 100000 -ref Mguttatus_genome.fa -sC 1 -eC 4942 -endPlugin -runfork1
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 5.1.0 Date: August 28, 2014
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Max Available Memory Reported by JVM: 9102 MB
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Java Version: 1.8.0_20
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -DiscoverySNPCallerPlugin, -i, pivotedTBT/pivotedTBT.h5, -m, topm/myMasterTags.topm, -o, hapmap/raw/myGBSGenos_chr+.hmp.txt, -mnF, -0.1, -mnMAF, 0.02, -mnMAC, 100000, -ref, Mguttatus_genome.fa, -sC, 1, -eC, 4942, -endPlugin, -runfork1]
net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
File = topm/myMasterTags.topm
TagMapFile Row Read:0
TagMapFile Row Read:1000000
TagMapFile Row Read:2000000
TagMapFile Row Read:3000000
TagMapFile Row Read:4000000
Count of Tags=4570190
initPhysicalSort
Position index sort begin.
Position index sort end.
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - minTaxaWithLocus:10 MinF:-0.100000 MinMAF:0.0200000 MinMAC:100000
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - includeRare:false includeGaps:false
[Thread-0] INFO net.maizegenetics.plugindef.AbstractPlugin -
DiscoverySNPCallerPlugin Parameters
i: pivotedTBT/pivotedTBT.h5
y: false
m: topm/myMasterTags.topm
o: hapmap/raw/myGBSGenos_chr+.hmp.txt
log: /mydata/GBS3/hapmap/raw/TagLocusLog.txt
mnF: -0.1
p: null
mnMAF: 0.02
mnMAC: 100000
mnLCov: 0.1
eR: 0.01
ref: Mguttatus_genome.fa
sC: 1
eC: 4942
inclRare: false
inclGaps: false
callBiSNPsWGap: false
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - Finding SNPs in pivotedTBT/pivotedTBT.h5.
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - StartChr:1 EndChr:4942
Starting Read Table Sort ...Done in 1304ms
initPhysicalSort
Position index sort begin.
Position index sort end.
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin -
As a check, here are the first 5 tags in the TOPM (sorted by position):
CTGCTTCTTTTCTTCTGAGATATATTCTCCTTCAGATATTTTCTTAGAATCAGTATCAACAGAT 64 1 1 1 19147 19210 1 * * * * * * * * * * * * * * * * * *
CTGCTTCTTTTCTTCTGAGATATATTCTCCTTCAGATGTTTTCTTAGAATCAGTATCAACAGAT 64 1 1 1 19147 19210 0 * * * * * * * * * * * * * * * * * *
CTGCCACTTTGGGTAGGAGATGTTTCATTCACGGCCTCATTCTCAGGTGATTCTGATGGTAAAA 64 1 1 1 19286 19349 0 * * * * * * * * * * * * * * * * * *
CTGCCACTTTGGGTAGGAGATGTTTCGTTCACGGCCTCATTCTCAGGTGATTCTGATGGTAAAA 64 1 1 1 19286 19349 1 * * * * * * * * * * * * * * * * * *
CAGCCCTATCCATGAGAGCCGAGCTGAAAAGGACTGTCTTGCAAATAGGAAGGAGAACTTTGTT 64 1 1 -1 19288 19225 0 * * * * * * * * * * * * * * * * * *
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin -
Processing chromosome 1...
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin -
Determining the length (in bases) of target chromosome 1 in the reference genome fasta file: Mguttatus_genome.fa
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - Currently reading chromosome 1 (target chromosome = 1)
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - The target chromosome 1 is 13654788 bases long
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin -
Reading in the target chromosome 1 from the reference genome fasta file: Mguttatus_genome.fa
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - Currently reading chromosome 1 (target chromosome = 1)
[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin -
Finished reading target chromosome 1 into a total of 426713 32bp chunks
Initializing the cutoffs for quantitative SNP calling likelihood ratio (pHet/pErr) >1
totalReadsForSNPInIndiv minLessTaggedAlleleCountForHet
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java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
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:686)
at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.discoverSNPsOnChromosome(DiscoverySNPCallerPlugin.java:632)
at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.processData(DiscoverySNPCallerPlugin.java:131)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:83)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1164)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
Caused by: 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.getScore(FractionalIdentityScorer.java:105)
at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53)
at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
java.util.concurrent.ExecutionException: java.lang.ExceptionInInitializerError
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
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:686)
at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.discoverSNPsOnChromosome(DiscoverySNPCallerPlugin.java:632)
at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.processData(DiscoverySNPCallerPlugin.java:131)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:83)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1164)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
Caused by: java.lang.ExceptionInInitializerError
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.getScore(FractionalIdentityScorer.java:105)
at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53)
at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
at java.util.Collections$UnmodifiableCollection.<init>(Collections.java:1026)
at java.util.Collections$UnmodifiableList.<init>(Collections.java:1302)
at java.util.Collections.unmodifiableList(Collections.java:1287)
at org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:111)
at org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:85)
at org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:57)
at org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:53)
at org.biojava3.core.sequence.location.template.Location.<clinit>(Location.java:48)
... 16 more
java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
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:686)
at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.discoverSNPsOnChromosome(DiscoverySNPCallerPlugin.java:632)
at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.processData(DiscoverySNPCallerPlugin.java:131)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:83)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1164)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
Caused by: 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.getScore(FractionalIdentityScorer.java:105)
at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53)
at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[Thread-0] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin: progress: 100%
[Thread-0] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.
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.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:686)
at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.discoverSNPsOnChromosome(DiscoverySNPCallerPlugin.java:632)
at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.processData(DiscoverySNPCallerPlugin.java:131)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:83)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1164)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
Jeff Glaubitz
Oct 1, 2014, 10:44:43 AM10/1/14
to tas...@googlegroups.com
Hi Alex,
I think the problem is that the biojava libraries were not replaced in the last release:
https://groups.google.com/forum/#!topic/tassel/jV3pKKLJ66c
This should be fixed in the next release.
Please note also that, in Tassel5, the DiscoverySNPCallerPlugin doesn’t output genotypes, but simply adds variants for the discovered SNPs to the TOPM (so -o now specifies an output TOPM with variants, not the genotype files). You must then use this output “Production TOPM” in the ProductionSNPCallerPlugin to obtain genotypes (in both hmp.txt.gz and hdf5 (h5) format. Please call the plugins without any arguments to see their usage.
Best,
Jeff
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Alex Twyford
Oct 1, 2014, 12:01:53 PM10/1/14
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Thanks Jeff!
When is the next release?
Alex
Terry Casstevens
Oct 1, 2014, 5:02:46 PM10/1/14
to Tassel User Group
Hi Alex,
If you are using Git to install Tassel 5, simply run "git pull" to
update. Otherwise, next release will be Thursday next week at the
earliest. We are currently working on major improvements which needs
to be tested.
Best,
Terry
If you are using Git to install Tassel 5, simply run "git pull" to
update. Otherwise, next release will be Thursday next week at the
earliest. We are currently working on major improvements which needs
to be tested.
Best,
Terry
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Alex Twyford
Oct 17, 2014, 6:08:10 AM10/17/14
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Hi Terry,
Any word on the new Tassel 5 release?
Thanks,
Alex
Terry Casstevens
Oct 17, 2014, 9:14:28 AM10/17/14
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Hi Alex,
We are still about two weeks away from another release. The native
installer is to big for me to send you an intermediate build. I could
send you just the sTASSEL.jar if you want. The git install option
will also get you the fix.
Best,
Terry
> https://groups.google.com/d/msgid/tassel/e7a240eb-37a6-47d2-afcf-05870d725db5%40googlegroups.com.
We are still about two weeks away from another release. The native
installer is to big for me to send you an intermediate build. I could
send you just the sTASSEL.jar if you want. The git install option
will also get you the fix.
Best,
Terry
Alex Twyford
Oct 21, 2014, 10:17:47 AM10/21/14
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Hi Terry,
Thanks for sharing the new biojava libraries, forester.jar and sTASSEL.jar. When I use them as you suggest, I get the error copied below. Any ideas?
Thanks,
Alex
Tassel5/lib/LiuExt.jar:Tassel5/lib/batik-awt-util.jar:Tassel5/lib/batik-css.jar:Tassel5/lib/batik-dom.jar:Tassel5/lib/batik-ext.jar:Tassel5/lib/batik-gui-util.jar:Tassel5/lib/batik-gvt.jar:Tassel5/lib/batik-parser.jar:Tassel5/lib/batik-svg-dom.jar:Tassel5/lib/batik-svggen.jar:Tassel5/lib/batik-util.jar:Tassel5/lib/batik-xml.jar:Tassel5/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:Tassel5/lib/colt.jar:Tassel5/lib/commons-math-2.2.jar:Tassel5/lib/ejml-0.23.jar:Tassel5/lib/forester.jar:Tassel5/lib/geronimo-spec-activation-1.0.2-rc4.jar:Tassel5/lib/guava-14.0.1.jar:Tassel5/lib/itextpdf-5.1.0.jar:Tassel5/lib/jcommon-1.0.6.jar:Tassel5/lib/jfreechart-1.0.3.jar:Tassel5/lib/json-simple-1.1.1.jar:Tassel5/lib/junit-4.10.jar:Tassel5/lib/log4j-1.2.13.jar:Tassel5/lib/mail-1.4.jar:Tassel5/lib/poi-3.0.1-FINAL-20070705.jar:Tassel5/lib/xercesImpl.jar:Tassel5/lib/xml.jar:Tassel5/lib/xmlParserAPIs.jar:Tassel5/lib/biojava3-alignment-4.0.0.jar:Tassel5/lib/biojava3-core-4.0.0.jar:Tassel5/lib/biojava3-phylo-4.0.0.jar:Tassel5/sTASSEL.jar
Memory Settings: -Xms512m -Xmx1536m
Tassel Pipeline Arguments:
Error: Could not find or load main class net.maizegenetics.pipeline.TasselPipeline
Terry Casstevens
Oct 21, 2014, 10:29:09 AM10/21/14
to Tassel User Group
Hi Alex,
Can you send me the command? Are you running it within the Tassel
directory? Not sure why your lib paths have Tassel5 in front of them?
Best,
Terry
Can you send me the command? Are you running it within the Tassel
directory? Not sure why your lib paths have Tassel5 in front of them?
Best,
Terry
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Alex Twyford
Oct 21, 2014, 11:19:15 AM10/21/14
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Hi Terry,
Sorry that was daft. Yes, you were right.
I'll let you know how it goes with the new BioJava libraries.
Thanks!
Alex
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