Re: GBS pipeline issue

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Terry Casstevens

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Mar 8, 2014, 1:27:00 AM3/8/14

to Aaron Chuah, Jeff Glaubitz, Tassel User Group

Hi Aaron,

Looks like a bug in the -hLD option. Probably need Jeff or Ed's input.

Terry

On Fri, Mar 7, 2014 at 2:34 AM, Aaron Chuah <Aaron...@anu.edu.au> wrote:
> Hi Terry & Jeff,
>
> Just realized it's been a full year since I last reported any TASSEL issues,
> despite running it for many datasets so far, which is kudos for your good
> work and constant improvements (can't wait to see the GBS/UNEAK pipelines
> implemented into 5 eventually!)
>
> Well, I'm writing because the IndexOutOfBounds bug has hit me again, this
> time at the very last stage of the GBS pipeline, namely:
>
> ./lib/junit-4.1.jar:./lib/commons-collections-3.1.jar:./lib/xercesImpl.jar:./lib/commons-logging-1.1.jar:./lib/batik-parser.jar:./lib/batik-ext.jar:./lib/XmlSchema-1.3.1.jar:./lib/xml.jar:./lib/batik-util.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/biojava3-core-3.0.jar:./lib/wsdl4j-1.6.2.jar:./lib/biojava3-alignment-3.0.jar:./lib/LiuExt.jar:./lib/mail-1.4.jar:./lib/mysql-connector-java-3.1.13-bin.jar:./lib/biojava3-phylo-3.0.jar:./lib/log4j-1.2.13.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/batik-xml.jar:./lib/jgrapht-0.5.3.jar:./lib/batik-svg-dom.jar:./lib/gdpc.jar:./lib/batik-awt-util.jar:./lib/batik-dom.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/axiom-impl-1.2.4.jar:./lib/commons-httpclient-3.0.1.jar:./lib/xmlParserAPIs.jar:./lib/batik-gui-util.jar:./lib/commons-lang-2.1.jar:./lib/batik-gvt.jar:./lib/lzma-4.63-jio-0.93.jar:./lib/jung-1.7.5.jar:./lib/ejml-0.13.jar:./lib/ssj.jar:./lib/batik-svggen.jar:./lib/commons-configuration-1.2.jar:./lib/crimson-parser.jar:./lib/jfreechart-1.0.3.jar:./lib/commons-codec-1.3.jar:./lib/commons-pool-1.3.jar:./lib/jcommon-1.0.6.jar:./lib/batik-css.jar:./lib/commons-dbcp-1.2.1.jar:./lib/axiom-api-1.2.4.jar:./lib/axis2-kernel-1.2.jar:./lib/forester.jar:./lib/colt.jar:./lib/commons-math-2.2.jar:./lib/commons-discovery.jar:./sTASSEL.jar
>
> Memory Settings: -Xms200g -Xmx201g
>
> Tassel Pipeline Arguments: -fork1 -GBSHapMapFiltersPlugin -hmp
> At_gbs/hapMap/mergedSNPs/At_gbs.mergedSNPs.c+.hmp.txt -o
> At_gbs/hapMap/filt/At_gbs.mergedSNPs.filt.c+.hmp.txt -hLD -mnTCov 0.05
> -mnSCov 0.05 -sC 1 -eC 7 -endPlugin -runfork1
>
> [main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version:
> 3.0.165 Date: January 16, 2014
>
> net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin
>
> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
> Reading: At_gbs/hapMap/mergedSNPs/At_gbs.mergedSNPs.c1.hmp.txt
>
> Time to count lines: 0
>
> Time to read file: 0
>
> Time to create Alignment: 0
>
> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
> Original Alignment Taxa:96 Sites:685
>
> RealDups ignoreHets ALL 0 0 NaN
>
> RandomDups ignoreHets ALL 0 0 NaN
>
> Percentile Coverage MAF F(inbreeding) GapProp
>
> 0.0 0.104 0.0172 -0.957 0.00
>
> 0.050 0.146 0.0351 -0.149 0.00
>
> 0.099 0.240 0.0377 -0.0874 0.00
>
> 0.15 0.354 0.0431 -0.0667 0.00
>
> 0.20 0.406 0.0446 -0.0625 0.00
>
> 0.25 0.448 0.0446 -0.0566 0.00
>
> 0.30 0.469 0.0484 -0.0515 0.00
>
> 0.35 0.500 0.0526 -0.0467 0.00
>
> 0.40 0.521 0.0545 -0.0467 0.00
>
> 0.45 0.542 0.0595 -0.0450 0.00
>
> 0.50 0.552 0.0625 -0.0392 0.00
>
> 0.55 0.573 0.0702 -0.0357 0.00
>
> 0.60 0.583 0.0833 -0.0175 0.00
>
> 0.65 0.583 0.0952 0.147 0.00
>
> 0.69 0.583 0.114 0.351 0.00
>
> 0.74 0.594 0.149 0.538 0.00
>
> 0.79 0.594 0.210 0.728 0.00
>
> 0.84 0.604 0.300 0.877 0.00
>
> 0.89 0.615 0.375 1.00 0.00
>
> 0.94 0.646 0.427 1.00 0.00
>
> 0.99 0.646 0.500 1.00 0.00
>
> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
> Ratio of RandomToReal:NaN
>
> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
> TaxaFiltered Alignment Taxa:62 Sites:685
>
> RealDups ignoreHets ALL 0 0 NaN
>
> RandomDups ignoreHets ALL 0 0 NaN
>
> Percentile Coverage MAF F(inbreeding) GapProp
>
> 0.0 0.161 0.0172 -0.957 0.00
>
> 0.050 0.226 0.0351 -0.149 0.00
>
> 0.099 0.371 0.0377 -0.0874 0.00
>
> 0.15 0.548 0.0431 -0.0667 0.00
>
> 0.20 0.629 0.0446 -0.0625 0.00
>
> 0.25 0.694 0.0446 -0.0566 0.00
>
> 0.30 0.726 0.0484 -0.0515 0.00
>
> 0.35 0.774 0.0526 -0.0467 0.00
>
> 0.40 0.806 0.0545 -0.0467 0.00
>
> 0.45 0.839 0.0595 -0.0450 0.00
>
> 0.50 0.855 0.0625 -0.0392 0.00
>
> 0.55 0.887 0.0702 -0.0357 0.00
>
> 0.60 0.903 0.0833 -0.0175 0.00
>
> 0.65 0.903 0.0952 0.147 0.00
>
> 0.69 0.903 0.114 0.351 0.00
>
> 0.74 0.919 0.149 0.538 0.00
>
> 0.79 0.919 0.210 0.728 0.00
>
> 0.84 0.935 0.300 0.877 0.00
>
> 0.89 0.952 0.375 1.00 0.00
>
> 0.94 1.00 0.427 1.00 0.00
>
> 0.99 1.00 0.500 1.00 0.00
>
> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
> Ratio of RandomToReal:NaN
>
> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
> SiteFiltered Alignment Taxa:62 Sites:685
>
> Entry1 Entry2 SNPDiff SNPsCompared PropDiff
>
> RealDups ignoreHets ALL 0 0 NaN
>
> RandomDups ignoreHets ALL 0 0 NaN
>
> 685 3 -2.00000 0.00000 NaN
>
> Percentile Coverage MAF F(inbreeding) GapProp
>
> 0.0 0.161 0.0172 -0.957 0.00
>
> 0.050 0.226 0.0351 -0.149 0.00
>
> 0.099 0.371 0.0377 -0.0874 0.00
>
> 0.15 0.548 0.0431 -0.0667 0.00
>
> 0.20 0.629 0.0446 -0.0625 0.00
>
> 0.25 0.694 0.0446 -0.0566 0.00
>
> 0.30 0.726 0.0484 -0.0515 0.00
>
> 0.35 0.774 0.0526 -0.0467 0.00
>
> 0.40 0.806 0.0545 -0.0467 0.00
>
> 0.45 0.839 0.0595 -0.0450 0.00
>
> 0.50 0.855 0.0625 -0.0392 0.00
>
> 0.55 0.887 0.0702 -0.0357 0.00
>
> 0.60 0.903 0.0833 -0.0175 0.00
>
> 0.65 0.903 0.0952 0.147 0.00
>
> 0.69 0.903 0.114 0.351 0.00
>
> 0.74 0.919 0.149 0.538 0.00
>
> 0.79 0.919 0.210 0.728 0.00
>
> 0.84 0.935 0.300 0.877 0.00
>
> 0.89 0.952 0.375 1.00 0.00
>
> 0.94 1.00 0.427 1.00 0.00
>
> 0.99 1.00 0.500 1.00 0.00
>
> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin - File
> written after basic
> filtering:At_gbs/hapMap/filt/At_gbs.mergedSNPs.filt.c1.hmp.txt
>
> Time to count lines: 0
>
> Time to read file: 0
>
> Time to create Alignment: 0
>
> Exception in thread "Thread-0" java.lang.ArrayIndexOutOfBoundsException: -50
>
> at
> net.maizegenetics.pal.popgen.LinkageDisequilibrium.getRSqr(LinkageDisequilibrium.java:567)
>
> at
> net.maizegenetics.gbs.pipeline.AlignmentFilterByGBSUtils.getGoodSitesByLD(AlignmentFilterByGBSUtils.java:214)
>
> at
> net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin.performFunction(GBSHapMapFiltersPlugin.java:106)
>
> at
> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>
> at
> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>
>
>
> I am running this on a fairly large-memory node (256GB), hence the -Xms200g
> -Xmx201g parameters to java, and I know throwing more memory at it won't
> solve an out of bounds exception, so I'm hoping to hear any pointers /
> suggestions that might help.
>
> Once again, thanks so much for your time.
>
> Sincerely,
> Aaron
>
> From: Terry Casstevens <tm...@cornell.edu>
> Date: Friday, March 1, 2013 at 6:16 PM
> To: Jeff Glaubitz <jcg...@cornell.edu>
> Cc: Aaron Chuah <aaron...@anu.edu.au>
> Subject: Re: GBS pipeline issue
>
>
> Hi Aaron,
>
> Please get the latest build of Tassel 3. Jon and I fixed some LD related
> issues since the January 10 build that you have. Please let me know if you
> still have problems with the new build.
>
> Cheers,
>
> Terry
>
>
>
> On Wed, Feb 27, 2013 at 5:01 PM, Jeff Glaubitz <jcg...@cornell.edu> wrote:
>>
>> Hi Aaron,
>>
>>
>>
>> You are right about both issues.
>>
>>
>>
>> As for your first issue, the pipeline is behaving as it is supposed to.
>> If the SNP caller (TagsToSNPByAlignmentPlugin) doesn't find any good SNPs on
>> a chromosome, it doesn't bother writing out a HapMap genotype file (which
>> would have been empty except for the header line). Subsequent steps (such
>> as MergeDuplicateSNPPlugin) try to open the missing file, but fail. So some
>> error messages are written out, but the exception is handled, so the program
>> just skips that chr and keeps going.
>>
>>
>>
>> As for the second issue, yes, it seems to be related to the small number
>> of sites in the chr6 file (108 SNPs). There is a hard coded fixed window
>> size for the LD testing of 100 sites (50 on either side). So 108 SNPs is
>> getting close to this window. However, even though we designed the pipeline
>> for chrs with large numbers of SNPs, this problem "should" be handled by the
>> code. I am not exactly sure why (or where) the bug occurs. I haven't tried
>> debugging yet (e.g., with a test alignment with only 108 SNPs in it).
>> Looking at the (Tassel3) code, I don't understand why it doesn't fail (with
>> an "java.lang.ArrayIndexOutOfBoundsException: -50" error) for every
>> chromosome for site 0 (i=0) and j = -50 at this step in
>> AlignmentFilterByGBSUtils (called by GBSHapMapFiltersPlugin):
>>
>>
>>
>> for(int j=i-(windowSize/2); j<i+(windowSize/2); j++) {
>>
>> if(Double.isNaN(theLD.getRSqr(i, j))) continue;
>>
>>
>>
>> But the LinkageDisequilibrium code is pretty complicated and I don't
>> understand all of it.
>>
>>
>>
>> Terry, do you have any ideas?
>>
>>
>>
>> Best,
>>
>>
>>
>> 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
>>
>>
>>
>> From: Aaron Chuah [mailto:Aaron...@anu.edu.au]
>> Sent: Tuesday, February 26, 2013 1:06 AM
>> To: Jeff Glaubitz
>> Subject: GBS pipeline issue
>>
>>
>>
>> Hi Jeff,
>>
>>
>>
>> Thanks for your help in the past, I hope all has been well over the winter
>> at Cornell.
>>
>>
>>
>> I'm sorry to have to trouble you again with an issue I've encountered
>> whilst running the GBS pipeline. There seem to be 2 (perhaps unrelated
>> issues), probably arising from the fact that the organism used
>> (brachypodium) has 83 supercontigs instead of a few chromosomes. Basically,
>> as shown in the red region below, it falters when it reaches "chromosome" 7
>> but is somehow ok again on a few of the subsequent chromosomes, like 51.
>> This suggests to me that when the hmp file generated happens to have no SNPs
>> within that chromosome, it complains, but processing is still ok,
>> downstream.
>>
>>
>>
>> The 2nd issue is right at the bottom in purple, where TASSEL throws an
>> ArrayIndexOutOfBoundsException this time, one chromosome earlier, at c6.
>> Could this be because the number of SNPs has passed some unstated threshold?
>> Might there be some switches I may apply to circumvent this problem?
>>
>>
>>
>> Thank you so much for your time and help.
>>
>>
>>
>> Sincerely,
>>
>> Aaron Chuah
>>
>> Genome Discovery Unit, John Curtin School of Medical Research,
>>
>> Australian National University
>>
>> --
>>
>>
>>
>>
>> ./lib/axiom-impl-1.2.4.jar:./lib/crimson-parser.jar:./lib/xml.jar:./lib/jcommon-1.0.6.jar:./lib/colt.jar:./lib/biojava3-core-3.0.jar:./lib/forester.jar:./lib/batik-util.jar:./lib/gdpc.jar:./lib/batik-parser.jar:./lib/commons-httpclient-3.0.1.jar:./lib/batik-gvt.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/XmlSchema-1.3.1.jar:./lib/ssj.jar:./lib/jfreechart-1.0.3.jar:./lib/commons-dbcp-1.2.1.jar:./lib/commons-codec-1.3.jar:./lib/jung-1.7.5.jar:./lib/commons-configuration-1.2.jar:./lib/commons-collections-3.1.jar:./lib/log4j-1.2.13.jar:./lib/batik-dom.jar:./lib/commons-pool-1.3.jar:./lib/commons-logging-1.1.jar:./lib/lzma-4.63-jio-0.93.jar:./lib/biojava3-phylo-3.0.jar:./lib/xmlParserAPIs.jar:./lib/wsdl4j-1.6.2.jar:./lib/batik-ext.jar:./lib/commons-math-2.2.jar:./lib/axis2-kernel-1.2.jar:./lib/axiom-api-1.2.4.jar:./lib/mysql-connector-java-3.1.13-bin.jar:./lib/batik-awt-util.jar:./lib/mail-1.4.jar:./lib/batik-svg-dom.jar:./lib/batik-xml.jar:./lib/jgrapht-0.5.3.jar:./lib/commons-discovery.jar:./lib/commons-lang-2.1.jar:./lib/junit-4.1.jar:./lib/batik-css.jar:./lib/batik-svggen.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/biojava3-alignment-3.0.jar:./lib/LiuExt.jar:./lib/ejml-0.13.jar:./lib/batik-gui-util.jar:./lib/xercesImpl.jar:./sTASSEL.jar
>>
>> Memory Settings: -Xms53g -Xmx54g
>>
>> Tassel Pipeline Arguments: -fork1 -MergeDuplicateSNPsPlugin -hmp
>> bd4_gbs/hapMap/unfilt/mergedTBT.c+.hmp.txt -o
>> bd4_gbs/hapMap/mergedSNPs/bd4_gbs.mergedSNPs.c+.hmp.txt -misMat 0.1
>> -callHets -s 1 -e 83 -endPlugin -runfork1
>>
>> [main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version:
>> 3.0.146 Date: January 10, 2013
>>
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c1.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Original Alignment Taxa:95 Sites:46912
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after merging duplicate SNPs: 46288
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after deleting any remaining, unmerged duplicate
>> SNPs: 45772
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c2.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Original Alignment Taxa:95 Sites:38353
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after merging duplicate SNPs: 37815
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after deleting any remaining, unmerged duplicate
>> SNPs: 37328
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c3.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Original Alignment Taxa:95 Sites:38541
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after merging duplicate SNPs: 37971
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after deleting any remaining, unmerged duplicate
>> SNPs: 37531
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c4.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Original Alignment Taxa:95 Sites:29797
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after merging duplicate SNPs: 29272
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after deleting any remaining, unmerged duplicate
>> SNPs: 28825
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c5.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Original Alignment Taxa:95 Sites:16993
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after merging duplicate SNPs: 16726
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after deleting any remaining, unmerged duplicate
>> SNPs: 16444
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c6.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Original Alignment Taxa:95 Sites:109
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after merging duplicate SNPs: 108
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after deleting any remaining, unmerged duplicate
>> SNPs: 108
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c7.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c7.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c7.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr7:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c7.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c8.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Original Alignment Taxa:95 Sites:2
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after merging duplicate SNPs: 2
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after deleting any remaining, unmerged duplicate
>> SNPs: 2
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c9.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c9.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c9.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr9:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c9.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c10.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c10.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c10.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr10:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c10.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c11.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c11.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c11.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr11:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c11.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c12.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Original Alignment Taxa:95 Sites:6
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after merging duplicate SNPs: 6
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after deleting any remaining, unmerged duplicate
>> SNPs: 6
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c13.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c13.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c13.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr13:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c13.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c14.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c14.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c14.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr14:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c14.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c15.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c15.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c15.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr15:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c15.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c16.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c16.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c16.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr16:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c16.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c17.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c17.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c17.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr17:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c17.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c18.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c18.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c18.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr18:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c18.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c19.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c19.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c19.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr19:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c19.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c20.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c20.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c20.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr20:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c20.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c21.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Original Alignment Taxa:95 Sites:14
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after merging duplicate SNPs: 14
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after deleting any remaining, unmerged duplicate
>> SNPs: 14
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c22.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c22.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c22.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr22:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c22.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c23.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c23.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c23.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr23:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c23.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c24.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c24.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c24.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr24:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c24.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c25.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c25.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c25.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr25:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c25.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c26.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c26.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c26.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr26:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c26.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c27.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c27.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c27.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr27:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c27.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c28.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c28.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c28.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr28:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c28.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c29.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c29.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c29.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr29:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c29.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c30.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c30.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c30.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr30:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c30.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c31.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c31.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c31.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr31:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c31.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c32.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c32.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c32.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr32:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c32.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c33.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c33.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c33.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr33:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c33.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c34.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c34.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c34.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr34:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c34.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c35.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c35.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c35.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr35:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c35.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c36.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c36.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c36.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr36:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c36.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c37.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c37.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c37.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr37:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c37.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c38.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c38.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c38.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr38:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c38.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c39.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c39.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c39.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr39:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c39.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c40.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c40.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c40.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr40:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c40.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c41.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c41.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c41.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr41:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c41.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c42.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c42.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c42.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr42:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c42.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c43.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c43.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c43.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr43:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c43.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c44.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c44.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c44.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr44:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c44.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c45.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c45.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c45.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr45:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c45.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c46.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c46.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c46.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr46:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c46.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c47.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c47.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c47.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr47:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c47.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c48.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c48.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c48.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr48:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c48.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c49.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c49.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c49.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr49:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c49.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c50.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c50.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c50.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr50:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c50.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c51.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Original Alignment Taxa:95 Sites:28
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after merging duplicate SNPs: 28
>>
>> initPhysicalSort
>>
>> Alignment sort begin.
>>
>> Alignment sort end.
>>
>> Number of sites written after deleting any remaining, unmerged duplicate
>> SNPs: 28
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c52.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c52.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c52.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr52:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c52.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c53.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c53.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c53.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr53:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c53.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c54.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c54.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c54.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr54:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c54.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c55.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c55.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c55.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr55:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c55.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c56.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c56.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c56.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr56:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c56.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c57.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c57.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c57.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr57:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c57.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c58.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c58.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c58.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr58:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c58.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c59.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c59.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c59.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr59:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c59.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c60.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c60.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c60.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr60:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c60.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c61.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c61.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c61.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr61:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c61.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c62.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c62.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c62.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr62:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c62.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c63.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c63.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c63.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr63:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c63.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c64.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c64.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c64.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr64:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c64.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c65.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c65.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c65.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr65:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c65.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c66.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c66.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c66.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr66:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c66.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c67.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c67.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c67.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr67:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c67.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c68.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c68.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c68.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr68:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c68.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c69.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c69.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c69.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr69:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c69.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c70.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c70.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c70.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr70:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c70.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c71.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c71.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c71.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr71:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c71.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c72.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c72.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c72.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr72:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c72.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c73.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c73.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c73.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr73:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c73.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c74.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c74.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c74.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr74:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c74.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c75.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c75.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c75.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr75:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c75.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c76.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c76.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c76.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr76:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c76.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c77.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c77.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c77.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr77:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c77.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c78.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c78.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c78.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr78:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c78.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c79.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c79.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c79.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr79:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c79.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c80.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c80.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c80.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr80:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c80.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c81.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c81.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c81.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr81:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c81.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c82.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c82.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c82.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr82:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c82.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Reading: bd4_gbs/hapMap/unfilt/mergedTBT.c83.hmp.txt
>>
>> [Thread-0] ERROR net.maizegenetics.util.Utils - getBufferedReader: Error
>> getting reader for: bd4_gbs/hapMap/unfilt/mergedTBT.c83.hmp.txt
>>
>> java.io.FileNotFoundException: bd4_gbs/hapMap/unfilt/mergedTBT.c83.hmp.txt
>> (No such file or directory)
>>
>> at java.io.FileInputStream.open(Native Method)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:137)
>>
>> at java.io.FileInputStream.<init>(FileInputStream.java:96)
>>
>> at net.maizegenetics.util.Utils.getBufferedReader(Utils.java:359)
>>
>> at
>> net.maizegenetics.pal.alignment.GdpdmBLOBUtils.getFileInfo(GdpdmBLOBUtils.java:268)
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:84)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> File IO in getFileInfo: java.lang.NullPointerException
>>
>> java.lang.NullPointerException
>>
>> at
>> net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:86)
>>
>> at
>> net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin.performFunction(MergeDuplicateSNPsPlugin.java:141)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.MergeDuplicateSNPsPlugin -
>> Could not read input hapmap file for chr83:
>>
>> bd4_gbs/hapMap/unfilt/mergedTBT.c83.hmp.txt
>>
>> e: java.lang.IllegalArgumentException: Problem creating Alignment: null
>>
>> Skipping...
>>
>>
>> ./lib/axiom-impl-1.2.4.jar:./lib/crimson-parser.jar:./lib/xml.jar:./lib/jcommon-1.0.6.jar:./lib/colt.jar:./lib/biojava3-core-3.0.jar:./lib/forester.jar:./lib/batik-util.jar:./lib/gdpc.jar:./lib/batik-parser.jar:./lib/commons-httpclient-3.0.1.jar:./lib/batik-gvt.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/XmlSchema-1.3.1.jar:./lib/ssj.jar:./lib/jfreechart-1.0.3.jar:./lib/commons-dbcp-1.2.1.jar:./lib/commons-codec-1.3.jar:./lib/jung-1.7.5.jar:./lib/commons-configuration-1.2.jar:./lib/commons-collections-3.1.jar:./lib/log4j-1.2.13.jar:./lib/batik-dom.jar:./lib/commons-pool-1.3.jar:./lib/commons-logging-1.1.jar:./lib/lzma-4.63-jio-0.93.jar:./lib/biojava3-phylo-3.0.jar:./lib/xmlParserAPIs.jar:./lib/wsdl4j-1.6.2.jar:./lib/batik-ext.jar:./lib/commons-math-2.2.jar:./lib/axis2-kernel-1.2.jar:./lib/axiom-api-1.2.4.jar:./lib/mysql-connector-java-3.1.13-bin.jar:./lib/batik-awt-util.jar:./lib/mail-1.4.jar:./lib/batik-svg-dom.jar:./lib/batik-xml.jar:./lib/jgrapht-0.5.3.jar:./lib/commons-discovery.jar:./lib/commons-lang-2.1.jar:./lib/junit-4.1.jar:./lib/batik-css.jar:./lib/batik-svggen.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/biojava3-alignment-3.0.jar:./lib/LiuExt.jar:./lib/ejml-0.13.jar:./lib/batik-gui-util.jar:./lib/xercesImpl.jar:./sTASSEL.jar
>>
>> Memory Settings: -Xms53g -Xmx54g
>>
>> Tassel Pipeline Arguments: -fork1 -GBSHapMapFiltersPlugin -hmp
>> bd4_gbs/hapMap/mergedSNPs/bd4_gbs.mergedSNPs.c+.hmp.txt -o
>> bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c+.hmp.txt -hLD -mnTCov 0.05
>> -mnSCov 0.05 -sC 1 -eC 83 -endPlugin -runfork1
>>
>> [main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version:
>> 3.0.146 Date: January 10, 2013
>>
>> net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Reading: bd4_gbs/hapMap/mergedSNPs/bd4_gbs.mergedSNPs.c1.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Original Alignment Taxa:95 Sites:45772
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.07370.00543
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.4320.0108
>>
>> -0.06150.00
>>
>> 0.10
>>
>> 0.7680.0108
>>
>> -0.04490.00
>>
>> 0.15
>>
>> 0.8210.0109
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.9050.0111
>>
>> -0.03370.00
>>
>> 0.25
>>
>> 0.9370.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9580.0161
>>
>> -0.02790.00
>>
>> 0.35
>>
>> 0.9680.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9680.0204
>>
>> -0.02470.00
>>
>> 0.45
>>
>> 0.9790.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 0.9790.0217
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 0.9790.0269
>>
>> -0.01710.00
>>
>> 0.60
>>
>> 0.9790.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 0.9790.0278
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 0.9790.0323
>>
>> -0.01320.00
>>
>> 0.75
>>
>> 0.9790.0333
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 0.9790.0380
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 0.9790.0449
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 0.9790.0611
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 0.9790.167
>>
>> 0.8360.00
>>
>> 1.0
>>
>> 0.9890.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> TaxaFiltered Alignment Taxa:93 Sites:45772
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.07530.00
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.4410.0108
>>
>> -0.06150.00
>>
>> 0.10
>>
>> 0.7850.0108
>>
>> -0.04490.00
>>
>> 0.15
>>
>> 0.8390.0109
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.9250.0111
>>
>> -0.03370.00
>>
>> 0.25
>>
>> 0.9570.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9780.0161
>>
>> -0.02790.00
>>
>> 0.35
>>
>> 0.9890.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9890.0204
>>
>> -0.02470.00
>>
>> 0.45
>>
>> 1.000.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 1.000.0217
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 1.000.0269
>>
>> -0.01710.00
>>
>> 0.60
>>
>> 1.000.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 1.000.0278
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 1.000.0323
>>
>> -0.01320.00
>>
>> 0.75
>>
>> 1.000.0333
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 1.000.0380
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 1.000.0449
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 1.000.0611
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 1.000.167
>>
>> 0.8360.00
>>
>> 1.0
>>
>> 1.000.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> SiteFiltered Alignment Taxa:93 Sites:45772
>>
>> Entry1 Entry2 SNPDiff SNPsCompared PropDiff
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> 45772 5 -2.00000 0.00000 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.07530.00
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.4410.0108
>>
>> -0.06150.00
>>
>> 0.10
>>
>> 0.7850.0108
>>
>> -0.04490.00
>>
>> 0.15
>>
>> 0.8390.0109
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.9250.0111
>>
>> -0.03370.00
>>
>> 0.25
>>
>> 0.9570.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9780.0161
>>
>> -0.02790.00
>>
>> 0.35
>>
>> 0.9890.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9890.0204
>>
>> -0.02470.00
>>
>> 0.45
>>
>> 1.000.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 1.000.0217
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 1.000.0269
>>
>> -0.01710.00
>>
>> 0.60
>>
>> 1.000.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 1.000.0278
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 1.000.0323
>>
>> -0.01320.00
>>
>> 0.75
>>
>> 1.000.0333
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 1.000.0380
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 1.000.0449
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 1.000.0611
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 1.000.167
>>
>> 0.8360.00
>>
>> 1.0
>>
>> 1.000.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c1.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> using sparse
>>
>> S1_11447 16 1.00000 1.00000 16.0000
>>
>> S1_1141662 73 1.00000 1.00000 73.0000
>>
>> S1_2536431 95 1.00000 0.0273312 2.59647
>>
>> S1_3940690 59 1.00000 0.0327285 1.93098
>>
>> S1_5858973 92 1.00000 0.00238118 0.219069
>>
>> S1_7190634 79 1.00000 0.0446885 3.53039
>>
>> S1_8964532 97 1.00000 2.30250e-14 2.23343e-12
>>
>> S1_10644650 57 1.00000 0.00198354 0.113062
>>
>> S1_12225000 48 1.00000 0.0441948 2.12135
>>
>> S1_13459132 34 1.00000 0.00461853 0.157030
>>
>> S1_14768836 35 1.00000 1.00000 35.0000
>>
>> S1_15814509 92 1.00000 0.105189 9.67742
>>
>> S1_17390933 69 1.00000 0.0140998 0.972888
>>
>> S1_18911223 96 1.00000 0.00502573 0.482470
>>
>> S1_20501686 93 1.00000 0.00977187 0.908784
>>
>> S1_22303466 75 1.00000 0.0447793 3.35845
>>
>> S1_23687406 83 1.00000 0.0844721 7.01118
>>
>> S1_25670091 85 1.00000 0.125526 10.6697
>>
>> S1_27284578 46 1.00000 0.0301000 1.38460
>>
>> S1_28362830 53 1.00000 0.135619 7.18780
>>
>> S1_30263715 56 1.00000 0.141825 7.94219
>>
>> S1_31614658 45 1.00000 0.115833 5.21249
>>
>> S1_33024411 72 1.00000 0.0248384 1.78836
>>
>> S1_35741802 65 1.00000 0.00911407 0.592414
>>
>> S1_38381142 71 1.00000 0.156609 11.1192
>>
>> S1_40571148 62 1.00000 0.0243902 1.51220
>>
>> S1_42845892 67 1.00000 0.0638149 4.27560
>>
>> S1_44727625 56 1.00000 0.0446885 2.50255
>>
>> S1_46057945 54 1.00000 0.415789 22.4526
>>
>> S1_47733912 69 1.00000 0.0198203 1.36760
>>
>> S1_49902568 53 1.00000 0.251780 13.3443
>>
>> S1_50807022 66 1.00000 0.0438722 2.89557
>>
>> S1_52546000 77 1.00000 0.0633737 4.87977
>>
>> S1_54188564 54 1.00000 0.0432394 2.33493
>>
>> S1_56301855 71 1.00000 0.237638 16.8723
>>
>> S1_57819695 32 1.00000 0.160967 5.15093
>>
>> S1_59610181 92 1.00000 0.0571755 5.26015
>>
>> S1_61234134 64 1.00000 0.0454545 2.90909
>>
>> S1_63246631 50 1.00000 0.0652015 3.26007
>>
>> S1_65145274 88 1.00000 0.0438722 3.86076
>>
>> S1_66755184 55 1.00000 0.0536838 2.95261
>>
>> S1_67856989 58 1.00000 0.145629 8.44647
>>
>> S1_69840951 53 1.00000 0.0638149 3.38219
>>
>> S1_71548020 53 1.00000 0.0854339 4.52799
>>
>> S1_72778712 58 1.00000 0.0149514 0.867181
>>
>> S1_73741683 57 1.00000 0.191750 10.9297
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> LDFiltered Alignment Taxa:93 Sites:1177
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic & LD
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c1.hmp.txt
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Reading: bd4_gbs/hapMap/mergedSNPs/bd4_gbs.mergedSNPs.c2.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Original Alignment Taxa:95 Sites:37328
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.09470.00543
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.4000.0108
>>
>> -0.06210.00
>>
>> 0.10
>>
>> 0.6950.0108
>>
>> -0.04490.00
>>
>> 0.15
>>
>> 0.8110.0108
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.8950.0110
>>
>> -0.03330.00
>>
>> 0.25
>>
>> 0.9370.0161
>>
>> -0.03080.00
>>
>> 0.30
>>
>> 0.9580.0161
>>
>> -0.02760.00
>>
>> 0.35
>>
>> 0.9680.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9680.0190
>>
>> -0.02270.00
>>
>> 0.45
>>
>> 0.9790.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 0.9790.0217
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 0.9790.0269
>>
>> -0.01680.00
>>
>> 0.60
>>
>> 0.9790.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 0.9790.0275
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 0.9790.0323
>>
>> -0.01160.00
>>
>> 0.75
>>
>> 0.9790.0337
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 0.9790.0380
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 0.9790.0471
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 0.9790.0682
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 0.9790.183
>>
>> 0.8770.00
>>
>> 1.0
>>
>> 0.9890.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> TaxaFiltered Alignment Taxa:93 Sites:37328
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.09680.00543
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.4090.0108
>>
>> -0.06210.00
>>
>> 0.10
>>
>> 0.7100.0108
>>
>> -0.04490.00
>>
>> 0.15
>>
>> 0.8280.0108
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.9140.0110
>>
>> -0.03330.00
>>
>> 0.25
>>
>> 0.9570.0161
>>
>> -0.03080.00
>>
>> 0.30
>>
>> 0.9780.0161
>>
>> -0.02760.00
>>
>> 0.35
>>
>> 0.9890.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9890.0190
>>
>> -0.02270.00
>>
>> 0.45
>>
>> 0.9890.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 1.000.0217
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 1.000.0269
>>
>> -0.01680.00
>>
>> 0.60
>>
>> 1.000.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 1.000.0275
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 1.000.0323
>>
>> -0.01160.00
>>
>> 0.75
>>
>> 1.000.0337
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 1.000.0380
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 1.000.0471
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 1.000.0682
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 1.000.183
>>
>> 0.8770.00
>>
>> 1.0
>>
>> 1.000.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> SiteFiltered Alignment Taxa:93 Sites:37328
>>
>> Entry1 Entry2 SNPDiff SNPsCompared PropDiff
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> 37328 5 -2.00000 0.00000 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.09680.00543
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.4090.0108
>>
>> -0.06210.00
>>
>> 0.10
>>
>> 0.7100.0108
>>
>> -0.04490.00
>>
>> 0.15
>>
>> 0.8280.0108
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.9140.0110
>>
>> -0.03330.00
>>
>> 0.25
>>
>> 0.9570.0161
>>
>> -0.03080.00
>>
>> 0.30
>>
>> 0.9780.0161
>>
>> -0.02760.00
>>
>> 0.35
>>
>> 0.9890.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9890.0190
>>
>> -0.02270.00
>>
>> 0.45
>>
>> 0.9890.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 1.000.0217
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 1.000.0269
>>
>> -0.01680.00
>>
>> 0.60
>>
>> 1.000.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 1.000.0275
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 1.000.0323
>>
>> -0.01160.00
>>
>> 0.75
>>
>> 1.000.0337
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 1.000.0380
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 1.000.0471
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 1.000.0682
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 1.000.183
>>
>> 0.8770.00
>>
>> 1.0
>>
>> 1.000.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c2.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> using sparse
>>
>> S2_9809 37 1.00000 1.00000 37.0000
>>
>> S2_1074287 47 1.00000 0.0915159 4.30125
>>
>> S2_1752712 0 -1.00000 1.00000 1.00000
>>
>> S2_2788890 69 1.00000 0.0951877 6.56795
>>
>> S2_3846097 80 1.00000 0.00685850 0.548680
>>
>> S2_5199764 58 1.00000 1.00000 58.0000
>>
>> S2_6456648 62 1.00000 0.105189 6.52174
>>
>> S2_7718586 64 1.00000 0.0303030 1.93939
>>
>> S2_9155701 46 1.00000 0.0606061 2.78788
>>
>> S2_10170918 93 1.00000 0.103158 9.59368
>>
>> S2_11841919 74 1.00000 0.0671350 4.96799
>>
>> S2_13688672 70 1.00000 0.0846190 5.92333
>>
>> S2_15234620 48 1.00000 0.223703 10.7377
>>
>> S2_17163403 64 1.00000 0.0250836 1.60535
>>
>> S2_18583729 75 1.00000 0.131982 9.89862
>>
>> S2_21252419 37 1.00000 1.00000 37.0000
>>
>> S2_23355049 53 1.00000 0.0209929 1.11262
>>
>> S2_25387278 55 1.00000 0.140665 7.73657
>>
>> S2_27165411 62 1.00000 0.00233754 0.144928
>>
>> S2_31391121 55 1.00000 0.0638149 3.50982
>>
>> S2_34410710 62 1.00000 0.125526 7.78261
>>
>> S2_36305412 66 1.00000 0.0107501 0.709508
>>
>> S2_38029875 55 1.00000 0.0645007 3.54754
>>
>> S2_39807765 66 1.00000 0.0952381 6.28571
>>
>> S2_41770400 73 1.00000 0.104794 7.64997
>>
>> S2_42991325 70 1.00000 0.183184 12.8229
>>
>> S2_44830150 73 1.00000 0.0821479 5.99679
>>
>> S2_46933870 30 1.00000 1.00000 30.0000
>>
>> S2_48448600 46 1.00000 1.00000 46.0000
>>
>> S2_49593708 66 1.00000 0.0473704 3.12645
>>
>> S2_50678490 62 1.00000 0.125526 7.78261
>>
>> S2_51978058 61 1.00000 0.0590979 3.60497
>>
>> S2_53461347 86 1.00000 0.00163934 0.140984
>>
>> S2_54944163 77 1.00000 0.0645007 4.96656
>>
>> S2_55722795 68 1.00000 0.0718585 4.88638
>>
>> S2_56914127 90 1.00000 0.176353 15.8718
>>
>> S2_58375168 71 1.00000 0.201335 14.2948
>>
>> S2_59180893 68 1.00000 0.0725806 4.93548
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> LDFiltered Alignment Taxa:93 Sites:1030
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic & LD
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c2.hmp.txt
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Reading: bd4_gbs/hapMap/mergedSNPs/bd4_gbs.mergedSNPs.c3.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Original Alignment Taxa:95 Sites:37531
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.08420.00543
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.3790.0108
>>
>> -0.06290.00
>>
>> 0.10
>>
>> 0.6630.0108
>>
>> -0.04550.00
>>
>> 0.15
>>
>> 0.8110.0109
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.9050.0111
>>
>> -0.03370.00
>>
>> 0.25
>>
>> 0.9370.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9580.0161
>>
>> -0.02760.00
>>
>> 0.35
>>
>> 0.9680.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9680.0204
>>
>> -0.02270.00
>>
>> 0.45
>>
>> 0.9790.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 0.9790.0217
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 0.9790.0269
>>
>> -0.01680.00
>>
>> 0.60
>>
>> 0.9790.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 0.9790.0278
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 0.9790.0323
>>
>> -0.01230.00
>>
>> 0.75
>>
>> 0.9790.0349
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 0.9790.0393
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 0.9790.0484
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 0.9790.0699
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 0.9790.185
>>
>> 0.8680.00
>>
>> 1.0
>>
>> 0.9890.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> TaxaFiltered Alignment Taxa:93 Sites:37531
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.08600.00543
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.3870.0108
>>
>> -0.06290.00
>>
>> 0.10
>>
>> 0.6770.0108
>>
>> -0.04550.00
>>
>> 0.15
>>
>> 0.8280.0109
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.9250.0111
>>
>> -0.03370.00
>>
>> 0.25
>>
>> 0.9570.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9780.0161
>>
>> -0.02760.00
>>
>> 0.35
>>
>> 0.9890.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9890.0204
>>
>> -0.02270.00
>>
>> 0.45
>>
>> 1.000.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 1.000.0217
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 1.000.0269
>>
>> -0.01680.00
>>
>> 0.60
>>
>> 1.000.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 1.000.0278
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 1.000.0323
>>
>> -0.01230.00
>>
>> 0.75
>>
>> 1.000.0349
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 1.000.0393
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 1.000.0484
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 1.000.0699
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 1.000.185
>>
>> 0.8680.00
>>
>> 1.0
>>
>> 1.000.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> SiteFiltered Alignment Taxa:93 Sites:37531
>>
>> Entry1 Entry2 SNPDiff SNPsCompared PropDiff
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> 37531 5 -2.00000 0.00000 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.08600.00543
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.3870.0108
>>
>> -0.06290.00
>>
>> 0.10
>>
>> 0.6770.0108
>>
>> -0.04550.00
>>
>> 0.15
>>
>> 0.8280.0109
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.9250.0111
>>
>> -0.03370.00
>>
>> 0.25
>>
>> 0.9570.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9780.0161
>>
>> -0.02760.00
>>
>> 0.35
>>
>> 0.9890.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9890.0204
>>
>> -0.02270.00
>>
>> 0.45
>>
>> 1.000.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 1.000.0217
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 1.000.0269
>>
>> -0.01680.00
>>
>> 0.60
>>
>> 1.000.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 1.000.0278
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 1.000.0323
>>
>> -0.01230.00
>>
>> 0.75
>>
>> 1.000.0349
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 1.000.0393
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 1.000.0484
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 1.000.0699
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 1.000.185
>>
>> 0.8680.00
>>
>> 1.0
>>
>> 1.000.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c3.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> using sparse
>>
>> S3_12781 21 1.00000 1.00000 21.0000
>>
>> S3_1152742 40 1.00000 0.100000 4.00000
>>
>> S3_2408453 88 1.00000 0.0164802 1.45025
>>
>> S3_3562666 48 1.00000 0.0521955 2.50539
>>
>> S3_5057777 65 1.00000 1.00000 65.0000
>>
>> S3_6847506 84 1.00000 0.0652015 5.47692
>>
>> S3_8324659 66 1.00000 0.0441948 2.91685
>>
>> S3_10378621 51 1.00000 0.492308 25.1077
>>
>> S3_12884411 93 1.00000 2.18510e-05 0.00203215
>>
>> S3_13991046 44 1.00000 0.000204243 0.00898671
>>
>> S3_15251407 67 1.00000 0.00524345 0.351311
>>
>> S3_16933572 85 1.00000 0.402904 34.2468
>>
>> S3_18892201 65 1.00000 0.0909091 5.90909
>>
>> S3_20444556 61 1.00000 0.0638149 3.89271
>>
>> S3_23059894 67 1.00000 0.0223233 1.49566
>>
>> S3_27596255 82 1.00000 0.0427770 3.50771
>>
>> S3_29707323 72 1.00000 0.0571755 4.11664
>>
>> S3_31934600 65 1.00000 0.0358902 2.33287
>>
>> S3_33784321 77 1.00000 0.124856 9.61387
>>
>> S3_35458175 51 1.00000 1.00000 51.0000
>>
>> S3_36778986 69 1.00000 0.130303 8.99091
>>
>> S3_39257451 76 1.00000 0.0641026 4.87180
>>
>> S3_40780213 32 1.00000 0.145629 4.66012
>>
>> S3_41812488 66 1.00000 0.00685850 0.452661
>>
>> S3_42315615 44 1.00000 0.0142857 0.628571
>>
>> S3_44052458 69 1.00000 0.203515 14.0426
>>
>> S3_45470561 81 1.00000 0.000751160 0.0608440
>>
>> S3_47417695 74 1.00000 0.0263158 1.94737
>>
>> S3_48406717 69 1.00000 0.0285037 1.96676
>>
>> S3_49955136 50 1.00000 0.0846190 4.23095
>>
>> S3_51374226 45 1.00000 1.00000 45.0000
>>
>> S3_52697323 64 1.00000 0.419355 26.8387
>>
>> S3_53817539 74 1.00000 0.0638149 4.72230
>>
>> S3_54805538 73 1.00000 0.0855232 6.24319
>>
>> S3_55795641 45 1.00000 0.0437118 1.96703
>>
>> S3_56929271 84 1.00000 0.196429 16.5000
>>
>> S3_58650786 45 1.00000 0.347293 15.6282
>>
>> S3_59398887 76 1.00000 0.0248440 1.88815
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> LDFiltered Alignment Taxa:93 Sites:1076
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic & LD
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c3.hmp.txt
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Reading: bd4_gbs/hapMap/mergedSNPs/bd4_gbs.mergedSNPs.c4.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Original Alignment Taxa:95 Sites:28825
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.09470.00543
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.3160.0108
>>
>> -0.06410.00
>>
>> 0.10
>>
>> 0.5260.0108
>>
>> -0.04760.00
>>
>> 0.15
>>
>> 0.7260.0109
>>
>> -0.03950.00
>>
>> 0.20
>>
>> 0.8210.0120
>>
>> -0.03450.00
>>
>> 0.25
>>
>> 0.8950.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9370.0161
>>
>> -0.02800.00
>>
>> 0.35
>>
>> 0.9470.0169
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9580.0215
>>
>> -0.02480.00
>>
>> 0.45
>>
>> 0.9680.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 0.9680.0227
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 0.9790.0269
>>
>> -0.01730.00
>>
>> 0.60
>>
>> 0.9790.0270
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 0.9790.0316
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 0.9790.0326
>>
>> -0.01220.00
>>
>> 0.75
>>
>> 0.9790.0376
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 0.9790.0430
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 0.9790.0517
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 0.9790.0769
>>
>> 0.2170.00
>>
>> 0.95
>>
>> 0.9790.194
>>
>> 0.8970.00
>>
>> 1.0
>>
>> 0.9790.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> TaxaFiltered Alignment Taxa:93 Sites:28825
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.09680.00543
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.3230.0108
>>
>> -0.06410.00
>>
>> 0.10
>>
>> 0.5380.0108
>>
>> -0.04760.00
>>
>> 0.15
>>
>> 0.7420.0109
>>
>> -0.03950.00
>>
>> 0.20
>>
>> 0.8390.0120
>>
>> -0.03450.00
>>
>> 0.25
>>
>> 0.9140.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9570.0161
>>
>> -0.02800.00
>>
>> 0.35
>>
>> 0.9680.0169
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9780.0215
>>
>> -0.02480.00
>>
>> 0.45
>>
>> 0.9890.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 0.9890.0227
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 1.000.0269
>>
>> -0.01730.00
>>
>> 0.60
>>
>> 1.000.0270
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 1.000.0316
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 1.000.0326
>>
>> -0.01220.00
>>
>> 0.75
>>
>> 1.000.0376
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 1.000.0430
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 1.000.0517
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 1.000.0769
>>
>> 0.2170.00
>>
>> 0.95
>>
>> 1.000.194
>>
>> 0.8970.00
>>
>> 1.0
>>
>> 1.000.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> SiteFiltered Alignment Taxa:93 Sites:28825
>>
>> Entry1 Entry2 SNPDiff SNPsCompared PropDiff
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> 28825 5 -2.00000 0.00000 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.09680.00543
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.3230.0108
>>
>> -0.06410.00
>>
>> 0.10
>>
>> 0.5380.0108
>>
>> -0.04760.00
>>
>> 0.15
>>
>> 0.7420.0109
>>
>> -0.03950.00
>>
>> 0.20
>>
>> 0.8390.0120
>>
>> -0.03450.00
>>
>> 0.25
>>
>> 0.9140.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9570.0161
>>
>> -0.02800.00
>>
>> 0.35
>>
>> 0.9680.0169
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9780.0215
>>
>> -0.02480.00
>>
>> 0.45
>>
>> 0.9890.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 0.9890.0227
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 1.000.0269
>>
>> -0.01730.00
>>
>> 0.60
>>
>> 1.000.0270
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 1.000.0316
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 1.000.0326
>>
>> -0.01220.00
>>
>> 0.75
>>
>> 1.000.0376
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 1.000.0430
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 1.000.0517
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 1.000.0769
>>
>> 0.2170.00
>>
>> 0.95
>>
>> 1.000.194
>>
>> 0.8970.00
>>
>> 1.0
>>
>> 1.000.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c4.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> using sparse
>>
>> S4_117757 49 1.00000 1.00000 49.0000
>>
>> S4_1287037 63 1.00000 0.0873908 5.50562
>>
>> S4_2418424 46 1.00000 0.0846190 3.89247
>>
>> S4_4163414 71 1.00000 0.00442629 0.314266
>>
>> S4_5501571 26 1.00000 1.00000 26.0000
>>
>> S4_6813506 52 1.00000 0.0439222 2.28396
>>
>> S4_7847403 66 1.00000 0.126167 8.32699
>>
>> S4_9103366 64 1.00000 0.00538972 0.344942
>>
>> S4_10095436 0 -1.00000 1.00000 1.00000
>>
>> S4_12144022 35 1.00000 0.0846190 2.96166
>>
>> S4_13769411 23 1.00000 0.0864469 1.98828
>>
>> S4_15434595 37 1.00000 0.153610 5.68356
>>
>> S4_17634870 69 1.00000 0.0446885 3.08350
>>
>> S4_20901081 68 1.00000 0.0714076 4.85572
>>
>> S4_23928758 40 1.00000 0.201335 8.05340
>>
>> S4_26407265 67 1.00000 0.0427770 2.86606
>>
>> S4_29046967 86 1.00000 0.0367347 3.15918
>>
>> S4_30989539 45 1.00000 0.0358902 1.61506
>>
>> S4_32129610 94 1.00000 0.154355 14.5093
>>
>> S4_33483511 83 1.00000 0.00432975 0.359369
>>
>> S4_35103439 70 1.00000 0.167164 11.7015
>>
>> S4_37173084 61 1.00000 0.306585 18.7017
>>
>> S4_37863415 62 1.00000 0.126167 7.82233
>>
>> S4_39377847 58 1.00000 0.128205 7.43590
>>
>> S4_41246035 46 1.00000 0.0427770 1.96774
>>
>> S4_42711635 51 1.00000 0.0904283 4.61185
>>
>> S4_44266989 60 1.00000 0.0750000 4.50000
>>
>> S4_46075162 83 1.00000 0.136975 11.3689
>>
>> S4_47477584 32 1.00000 0.241249 7.71996
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> LDFiltered Alignment Taxa:93 Sites:958
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic & LD
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c4.hmp.txt
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Reading: bd4_gbs/hapMap/mergedSNPs/bd4_gbs.mergedSNPs.c5.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Original Alignment Taxa:95 Sites:16444
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.07370.00568
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.3680.0108
>>
>> -0.06590.00
>>
>> 0.10
>>
>> 0.6210.0108
>>
>> -0.04550.00
>>
>> 0.15
>>
>> 0.7890.0109
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.8740.0112
>>
>> -0.03370.00
>>
>> 0.25
>>
>> 0.9260.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9470.0161
>>
>> -0.02760.00
>>
>> 0.35
>>
>> 0.9580.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9680.0197
>>
>> -0.02300.00
>>
>> 0.45
>>
>> 0.9680.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 0.9790.0220
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 0.9790.0269
>>
>> -0.01680.00
>>
>> 0.60
>>
>> 0.9790.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 0.9790.0283
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 0.9790.0323
>>
>> -0.01190.00
>>
>> 0.75
>>
>> 0.9790.0362
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 0.9790.0400
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 0.9790.0484
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 0.9790.0703
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 0.9790.183
>>
>> 0.8820.00
>>
>> 1.0
>>
>> 0.9890.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> TaxaFiltered Alignment Taxa:93 Sites:16444
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.07530.00568
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.3760.0108
>>
>> -0.06590.00
>>
>> 0.10
>>
>> 0.6340.0108
>>
>> -0.04550.00
>>
>> 0.15
>>
>> 0.8060.0109
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.8920.0112
>>
>> -0.03370.00
>>
>> 0.25
>>
>> 0.9460.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9680.0161
>>
>> -0.02760.00
>>
>> 0.35
>>
>> 0.9780.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9890.0197
>>
>> -0.02300.00
>>
>> 0.45
>>
>> 0.9890.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 1.000.0220
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 1.000.0269
>>
>> -0.01680.00
>>
>> 0.60
>>
>> 1.000.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 1.000.0283
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 1.000.0323
>>
>> -0.01190.00
>>
>> 0.75
>>
>> 1.000.0362
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 1.000.0400
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 1.000.0484
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 1.000.0703
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 1.000.183
>>
>> 0.8820.00
>>
>> 1.0
>>
>> 1.000.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> SiteFiltered Alignment Taxa:93 Sites:16444
>>
>> Entry1 Entry2 SNPDiff SNPsCompared PropDiff
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> 16444 5 -2.00000 0.00000 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.07530.00568
>>
>> -1.000.00
>>
>> 0.050
>>
>> 0.3760.0108
>>
>> -0.06590.00
>>
>> 0.10
>>
>> 0.6340.0108
>>
>> -0.04550.00
>>
>> 0.15
>>
>> 0.8060.0109
>>
>> -0.03910.00
>>
>> 0.20
>>
>> 0.8920.0112
>>
>> -0.03370.00
>>
>> 0.25
>>
>> 0.9460.0161
>>
>> -0.03330.00
>>
>> 0.30
>>
>> 0.9680.0161
>>
>> -0.02760.00
>>
>> 0.35
>>
>> 0.9780.0163
>>
>> -0.02760.00
>>
>> 0.40
>>
>> 0.9890.0197
>>
>> -0.02300.00
>>
>> 0.45
>>
>> 0.9890.0215
>>
>> -0.02200.00
>>
>> 0.50
>>
>> 1.000.0220
>>
>> -0.02200.00
>>
>> 0.55
>>
>> 1.000.0269
>>
>> -0.01680.00
>>
>> 0.60
>>
>> 1.000.0269
>>
>> -0.01640.00
>>
>> 0.65
>>
>> 1.000.0283
>>
>> -0.01640.00
>>
>> 0.70
>>
>> 1.000.0323
>>
>> -0.01190.00
>>
>> 0.75
>>
>> 1.000.0362
>>
>> -0.01100.00
>>
>> 0.80
>>
>> 1.000.0400
>>
>> -0.01090.00
>>
>> 0.85
>>
>> 1.000.0484
>>
>> -0.01090.00
>>
>> 0.90
>>
>> 1.000.0703
>>
>> -0.01090.00
>>
>> 0.95
>>
>> 1.000.183
>>
>> 0.8820.00
>>
>> 1.0
>>
>> 1.000.500
>>
>> 1.000.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c5.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> using sparse
>>
>> S5_247700 45 1.00000 1.00000 45.0000
>>
>> S5_2010388 80 1.00000 0.0167832 1.34266
>>
>> S5_4132663 96 1.00000 1.05990e-05 0.00101750
>>
>> S5_7239995 58 1.00000 0.171123 9.92513
>>
>> S5_10530786 76 1.00000 0.0854305 6.49272
>>
>> S5_13746542 73 1.00000 0.0950456 6.93833
>>
>> S5_15611883 72 1.00000 0.0638149 4.59467
>>
>> S5_17038047 91 1.00000 0.139332 12.6792
>>
>> S5_18493063 55 1.00000 1.00000 55.0000
>>
>> S5_20205643 38 1.00000 1.00000 38.0000
>>
>> S5_21526018 37 1.00000 0.0378357 1.39992
>>
>> S5_22642937 65 1.00000 0.0517241 3.36207
>>
>> S5_23845102 34 1.00000 0.125526 4.26788
>>
>> S5_24928513 99 1.00000 0.129588 12.8292
>>
>> S5_25726023 61 1.00000 0.105189 6.41655
>>
>> S5_26781832 72 1.00000 0.0638149 4.59467
>>
>> S5_27693751 49 1.00000 0.105189 5.15428
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> LDFiltered Alignment Taxa:93 Sites:423
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic & LD
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c5.hmp.txt
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Reading: bd4_gbs/hapMap/mergedSNPs/bd4_gbs.mergedSNPs.c6.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Original Alignment Taxa:95 Sites:108
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.8210.0108
>>
>> -0.8060.00
>>
>> 0.046
>>
>> 0.9260.0108
>>
>> -0.1340.00
>>
>> 0.093
>>
>> 0.9470.0108
>>
>> -0.06900.00
>>
>> 0.14
>>
>> 0.9580.0161
>>
>> -0.05080.00
>>
>> 0.19
>>
>> 0.9680.0161
>>
>> -0.04650.00
>>
>> 0.23
>>
>> 0.9680.0165
>>
>> -0.04190.00
>>
>> 0.28
>>
>> 0.9790.0215
>>
>> -0.03410.00
>>
>> 0.32
>>
>> 0.9790.0215
>>
>> -0.03330.00
>>
>> 0.37
>>
>> 0.9790.0217
>>
>> -0.03330.00
>>
>> 0.42
>>
>> 0.9790.0269
>>
>> -0.02860.00
>>
>> 0.46
>>
>> 0.9790.0269
>>
>> -0.02760.00
>>
>> 0.51
>>
>> 0.9790.0281
>>
>> -0.02760.00
>>
>> 0.56
>>
>> 0.9790.0323
>>
>> -0.02220.00
>>
>> 0.60
>>
>> 0.9790.0323
>>
>> -0.02200.00
>>
>> 0.65
>>
>> 0.9790.0376
>>
>> -0.02200.00
>>
>> 0.69
>>
>> 0.9790.0430
>>
>> -0.01640.00
>>
>> 0.74
>>
>> 0.9790.0455
>>
>> -0.01640.00
>>
>> 0.79
>>
>> 0.9790.0538
>>
>> -0.01640.00
>>
>> 0.83
>>
>> 0.9790.0645
>>
>> -0.01090.00
>>
>> 0.88
>>
>> 0.9790.159
>>
>> -0.01090.00
>>
>> 0.93
>>
>> 0.9790.231
>>
>> -0.008660.00
>>
>> 0.97
>>
>> 0.9790.344
>>
>> 0.8570.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> TaxaFiltered Alignment Taxa:93 Sites:108
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.8390.0108
>>
>> -0.8060.00
>>
>> 0.046
>>
>> 0.9460.0108
>>
>> -0.1340.00
>>
>> 0.093
>>
>> 0.9680.0108
>>
>> -0.06900.00
>>
>> 0.14
>>
>> 0.9780.0161
>>
>> -0.05080.00
>>
>> 0.19
>>
>> 0.9890.0161
>>
>> -0.04650.00
>>
>> 0.23
>>
>> 0.9890.0165
>>
>> -0.04190.00
>>
>> 0.28
>>
>> 1.000.0215
>>
>> -0.03410.00
>>
>> 0.32
>>
>> 1.000.0215
>>
>> -0.03330.00
>>
>> 0.37
>>
>> 1.000.0217
>>
>> -0.03330.00
>>
>> 0.42
>>
>> 1.000.0269
>>
>> -0.02860.00
>>
>> 0.46
>>
>> 1.000.0269
>>
>> -0.02760.00
>>
>> 0.51
>>
>> 1.000.0281
>>
>> -0.02760.00
>>
>> 0.56
>>
>> 1.000.0323
>>
>> -0.02220.00
>>
>> 0.60
>>
>> 1.000.0323
>>
>> -0.02200.00
>>
>> 0.65
>>
>> 1.000.0376
>>
>> -0.02200.00
>>
>> 0.69
>>
>> 1.000.0430
>>
>> -0.01640.00
>>
>> 0.74
>>
>> 1.000.0455
>>
>> -0.01640.00
>>
>> 0.79
>>
>> 1.000.0538
>>
>> -0.01640.00
>>
>> 0.83
>>
>> 1.000.0645
>>
>> -0.01090.00
>>
>> 0.88
>>
>> 1.000.159
>>
>> -0.01090.00
>>
>> 0.93
>>
>> 1.000.231
>>
>> -0.008660.00
>>
>> 0.97
>>
>> 1.000.344
>>
>> 0.8570.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> Ratio of RandomToReal:NaN
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> SiteFiltered Alignment Taxa:93 Sites:108
>>
>> Entry1 Entry2 SNPDiff SNPsCompared PropDiff
>>
>> RealDups ignoreHets ALL 0 0 NaN
>>
>> RandomDups ignoreHets ALL 0 0 NaN
>>
>> 108 5 -2.00000 0.00000 NaN
>>
>> Percentile
>>
>> CoverageMAF
>>
>> F(inbreeding) GapProp
>>
>> 0.0
>>
>> 0.8390.0108
>>
>> -0.8060.00
>>
>> 0.046
>>
>> 0.9460.0108
>>
>> -0.1340.00
>>
>> 0.093
>>
>> 0.9680.0108
>>
>> -0.06900.00
>>
>> 0.14
>>
>> 0.9780.0161
>>
>> -0.05080.00
>>
>> 0.19
>>
>> 0.9890.0161
>>
>> -0.04650.00
>>
>> 0.23
>>
>> 0.9890.0165
>>
>> -0.04190.00
>>
>> 0.28
>>
>> 1.000.0215
>>
>> -0.03410.00
>>
>> 0.32
>>
>> 1.000.0215
>>
>> -0.03330.00
>>
>> 0.37
>>
>> 1.000.0217
>>
>> -0.03330.00
>>
>> 0.42
>>
>> 1.000.0269
>>
>> -0.02860.00
>>
>> 0.46
>>
>> 1.000.0269
>>
>> -0.02760.00
>>
>> 0.51
>>
>> 1.000.0281
>>
>> -0.02760.00
>>
>> 0.56
>>
>> 1.000.0323
>>
>> -0.02220.00
>>
>> 0.60
>>
>> 1.000.0323
>>
>> -0.02200.00
>>
>> 0.65
>>
>> 1.000.0376
>>
>> -0.02200.00
>>
>> 0.69
>>
>> 1.000.0430
>>
>> -0.01640.00
>>
>> 0.74
>>
>> 1.000.0455
>>
>> -0.01640.00
>>
>> 0.79
>>
>> 1.000.0538
>>
>> -0.01640.00
>>
>> 0.83
>>
>> 1.000.0645
>>
>> -0.01090.00
>>
>> 0.88
>>
>> 1.000.159
>>
>> -0.01090.00
>>
>> 0.93
>>
>> 1.000.231
>>
>> -0.008660.00
>>
>> 0.97
>>
>> 1.000.344
>>
>> 0.8570.00
>>
>> [Thread-0] INFO net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin -
>> File written after basic
>> filtering:bd4_gbs/hapMap/filt/bd4_gbs.mergedSNPs.filt.c6.hmp.txt
>>
>> Time to count lines: 0
>>
>> Time to read file: 0
>>
>> Time to create Alignment: 0
>>
>> Exception in thread "Thread-0" java.lang.ArrayIndexOutOfBoundsException:
>> -50
>>
>> at
>> net.maizegenetics.pal.popgen.LinkageDisequilibrium.getRSqr(LinkageDisequilibrium.java:547)
>>
>> at
>> net.maizegenetics.gbs.pipeline.AlignmentFilterByGBSUtils.getGoodSitesByLD(AlignmentFilterByGBSUtils.java:214)
>>
>> at
>> net.maizegenetics.gbs.pipeline.GBSHapMapFiltersPlugin.performFunction(GBSHapMapFiltersPlugin.java:106)
>>
>> at
>> net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
>>
>> at
>> net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
>
>

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