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Analysis failed - getting JAVA errors:groovy.lang.MissingMethodException: No signature of method: groovy.util.ConfigObject.MOPs() #17

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SafinaAr opened this issue Nov 7, 2018 · 16 comments
Open

Analysis failed - getting JAVA errors:groovy.lang.MissingMethodException: No signature of method: groovy.util.ConfigObject.MOPs() #17

SafinaAr opened this issue Nov 7, 2018 · 16 comments

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@SafinaAr
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SafinaAr commented Nov 7, 2018

Im running the analysis on 14 BAM files 7 from tumor and 7 from its germline. which is in a
/mnt/d/AKU/FTP/BAM/.

I rand the following command to test the tool:
./ximmer -v -nosim -c /mnt/d/AKU/FTP/BAM/config.groovy -o results

This is my config.groovy file:

bam_files="/mnt/d/AKU/FTP/BAM/*.bam"
target_regions="/mnt/d/AKU/FTP/BAM/TruSeq_exome_targeted_regions.hg19.bed"
concurrency=20
callers {
    cn.MOPs {}
    exomedepth {}
        Conifer {}
}

After Running im getting the following error:

Configured verbose logging
Ximmer  [1]     INFO    |6:51:57 Configured verbose logging
Caught: groovy.lang.MissingMethodException: No signature of method: groovy.util.ConfigObject.MOPs() is applicable for argument types: (script1541573517941211209064$_run_closure1$_closure2) values: [script1541573517941211209064$_run_closure1$_closure2@4b34fff9]
Possible solutions: sort(), is(java.lang.Object), plus(java.util.Collection), plus(java.util.Map), wait(), size()
groovy.lang.MissingMethodException: No signature of method: groovy.util.ConfigObject.MOPs() is applicable for argument types: (script1541573517941211209064$_run_closure1$_closure2) values: [script1541573517941211209064$_run_closure1$_closure2@4b34fff9]
Possible solutions: sort(), is(java.lang.Object), plus(java.util.Collection), plus(java.util.Map), wait(), size()
        at script1541573517941211209064$_run_closure1.doCall(script1541573517941211209064.groovy:5)
        at script1541573517941211209064$_run_closure1.doCall(script1541573517941211209064.groovy)
        at script1541573517941211209064.run(script1541573517941211209064.groovy:4)
        at Ximmer.main(Ximmer.groovy:1266)

While installing XIMMER i was unable to install xhmm only all other were success and i was also unable to solve the xhmm error which is:

In file included from sources/lib/MatrixDecomp.cpp:3:0:
./sources/include/VectorOnDisk.hpp: In instantiation of ‘HMM_PP::VectorOnDisk<dataType>::~VectorOnDisk() [with dataType = double]’:
sources/lib/MatrixDecomp.cpp:75:1:   required from here
./sources/include/VectorOnDisk.hpp:91:37: error: throw will always call terminate() [-Werror=terminate]
        throw new Exception(str.str());
                                     ^
./sources/include/VectorOnDisk.hpp:91:37: note: in C++11 destructors default to noexcept
cc1plus: all warnings being treated as errors
config_rules.Makefile:16: recipe for target 'build/lib/MatrixDecomp.o' failed
make[2]: *** [build/lib/MatrixDecomp.o] Error 1
make[2]: Leaving directory '/home/sark/ximmer/eval/pipeline/tools/xhmm/statgen-xhmm-cc14e528d909/sources/hmm++'
Makefile:126: recipe for target 'sources/hmm++/' failed
make[1]: *** [sources/hmm++/] Error 2
make[1]: Leaving directory '/home/sark/ximmer/eval/pipeline/tools/xhmm/statgen-xhmm-cc14e528d909'
Makefile:121: recipe for target 'all' failed
make: *** [all] Error 2

Can you please help?
@SafinaAr
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SafinaAr commented Nov 7, 2018

I also tried to build gradlew present in the ximmer folder getting these errors:

:compileGroovy
startup failed:
/home/sark/ximmer/src/main/groovy/AngelResults.groovy: 4: unable to resolve class gngs.RangedData
 @ line 4, column 1.
   import gngs.RangedData
   ^

/home/sark/ximmer/src/main/groovy/CNMopsResults.groovy: 5: unable to resolve class gngs.RangedData
 @ line 5, column 1.
   import gngs.RangedData
   ^

/home/sark/ximmer/src/main/groovy/CNMopsResults.groovy: 6: unable to resolve class gngs.Region
 @ line 6, column 1.
   import gngs.Region
   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 8: unable to resolve class org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction
 @ line 8, column 1.
   import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction
   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 7: unable to resolve class org.apache.commons.math3.analysis.interpolation.LoessInterpolator
 @ line 7, column 1.
   import org.apache.commons.math3.analysis.interpolation.LoessInterpolator
   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 20: unable to resolve class htsjdk.samtools.SamReader
 @ line 20, column 1.
   import htsjdk.samtools.SamReader
   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 13: unable to resolve class graxxia.Matrix
 @ line 13, column 1.
   import graxxia.Matrix
   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 14: unable to resolve class graxxia.Stats
 @ line 14, column 1.
   import graxxia.Stats
   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 39: unable to resolve class SampleInfo
 @ line 39, column 16.
       Map<String,SampleInfo> sampleInfo
                  ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 41: unable to resolve class Regions
 @ line 41, column 5.
       Regions cnvs
       ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 56: unable to resolve class SAM
 @ line 56, column 16.
       Map<String,SAM> bams
                  ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 61: unable to resolve class RangedData
 @ line 61, column 17.
       Map<String, RangedData> cnvCalls
                   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 69: unable to resolve class RefGenes
 @ line 69, column 5.
       RefGenes geneDb = null
       ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 71: unable to resolve class Regions
 @ line 71, column 5.
       Regions targetRegions = null
       ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 73: unable to resolve class Regions
 @ line 73, column 16.
       Map<String,Regions> vcfs = Collections.synchronizedMap([:])
                  ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 78: unable to resolve class Regions
 @ line 78, column 5.
       Regions amplicons = null
       ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 762: unable to resolve class htsjdk.samtools.SamReader
 @ line 762, column 29.
       ThreadLocal<Map<String, SamReader>> readers = new ThreadLocal()
                               ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 112: unable to resolve class Regions
 @ line 112, column 16.
       CNVDiagram(Regions cnvs, Map<String,SampleInfo> sampleInfo, Map<String, RangedData> cnvCalls, Regions targetRegions, List<String> vcfFiles, List<String> samples=null) {
                  ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 112: unable to resolve class SampleInfo
 @ line 112, column 41.
   gram(Regions cnvs, Map<String,SampleInfo
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 112: unable to resolve class RangedData
 @ line 112, column 77.
   Info> sampleInfo, Map<String, RangedData
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 112: unable to resolve class Regions
 @ line 112, column 99.
   String, RangedData> cnvCalls, Regions ta
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 131: unable to resolve class VCF
 @ line 131, column 14.
           List<VCF> vcfs = vcfFiles.collect { VCF.parse(it) { cnvs.overlaps(it) } }
                ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 133: unable to resolve class VCF
 @ line 133, column 13.
           Map<VCF, Regions> vcfRegions = vcfs.collectEntries { [ it,  it.toRegions() ] }
               ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 133: unable to resolve class Regions
 @ line 133, column 18.
           Map<VCF, Regions> vcfRegions = vcfs.collectEntries { [ it,  it.toRegions() ] }
                    ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 136: unable to resolve class VCF
 @ line 136, column 17.
               VCF sampleVCF = vcfs.find { sample in it.samples }
                   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 142: unable to resolve class SAM
 @ line 142, column 14.
           List<SAM> sampleBams = allSamples.collect { String sample ->
                ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 147: unable to resolve class SAM
 @ line 147, column 13.
               new SAM(sampleInfo[sample].files.bam[0])
               ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 161: unable to resolve class Regions
 @ line 161, column 21.
               Regions meanRegions = targetRegions
                       ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 243: unable to resolve class Region
 @ line 243, column 18.
       void drawCNV(Region cnv, String outputFileBase, int width, int height, List callers, Map colors) {
                    ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 284: unable to resolve class SAM
 @ line 284, column 13.
           SAM bam = bams[cnv.sample]
               ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 298: unable to resolve class Region
 @ line 298, column 16.
           Region displayRegion = new Region(cnv.chr, froms[0]..tos[-1])
                  ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 298: unable to resolve class Region
 @ line 298, column 32.
           Region displayRegion = new Region(cnv.chr, froms[0]..tos[-1])
                                  ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 303: unable to resolve class graxxia.Drawing
 @ line 303, column 25.
           graxxia.Drawing d
                           ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 312: unable to resolve class Region
 @ line 312, column 20.
               Region targetRegion = new Region(cnv.chr, target)
                      ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 312: unable to resolve class Region
 @ line 312, column 35.
               Region targetRegion = new Region(cnv.chr, target)
                                     ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 444: unable to resolve class graxxia.Drawing
 @ line 444, column 35.
       void drawInterpolatedCoverage(graxxia.Drawing d, Matrix coverage, IntRange target, double [] targetRange) {
                                     ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 465: unable to resolve class graxxia.Drawing
 @ line 465, column 36.
       void drawVariants(Writer json, graxxia.Drawing d, Region cnv, List<IntRange> targets) {
                                      ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 465: unable to resolve class Region
 @ line 465, column 55.
   iter json, graxxia.Drawing d, Region cnv
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 467: unable to resolve class Regions
 @ line 467, column 17.
           Regions vcf = vcfs[cnv.sample]
                   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 476: unable to resolve class Variant
 @ line 476, column 9.
           for(Variant variant in variants) {
           ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 514: unable to resolve class Region
 @ line 514, column 48.
   rgetJSONCoverage(Writer json, Region tar
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 525: unable to resolve class Region
 @ line 525, column 62.
   amFrame(String imageFileName, Region dis
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 525: unable to resolve class graxxia.Drawing
 @ line 525, column 5.
       graxxia.Drawing createDiagramFrame(String imageFileName, Region displayRegion, List<IntRange> targets, int width, int height) {
       ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 530: unable to resolve class graxxia.Drawing
 @ line 530, column 25.
           graxxia.Drawing d = new graxxia.Drawing(
                           ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 530: unable to resolve class graxxia.Drawing
 @ line 530, column 29.
           graxxia.Drawing d = new graxxia.Drawing(
                               ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 567: unable to resolve class Region
 @ line 567, column 40.
       List<IntRange> determineCnvTargets(Region rawCNV, List<String> genes) {
                                          ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 578: unable to resolve class Region
 @ line 578, column 16.
           Region cnv = new Region(rawCNV.chr, cnvTargetIntersect[0].from, cnvTargetIntersect[-1].to)
                  ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 578: unable to resolve class Region
 @ line 578, column 22.
           Region cnv = new Region(rawCNV.chr, cnvTargetIntersect[0].from, cnvTargetIntersect[-1].to)
                        ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 619: unable to resolve class Region
 @ line 619, column 28.
       List<Range> padTargets(Region cnv, List<Range> targets) {
                              ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 659: unable to resolve class Region
 @ line 659, column 67.
   xonsRange(List<String> genes, Region cnv
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 661: unable to resolve class Regions
 @ line 661, column 17.
           Regions geneExons = genes.sum { geneDb.getExons(it) }.reduce().grep { it.chr == cnv.chr } as Regions
                   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 661: unable to resolve class Regions
 @ line 661, column 99.
   ().grep { it.chr == cnv.chr } as Regions
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 689: unable to resolve class graxxia.Drawing
 @ line 689, column 24.
       void drawAmplicons(graxxia.Drawing d, Region cnv) {
                          ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 689: unable to resolve class Region
 @ line 689, column 43.
   wAmplicons(graxxia.Drawing d, Region cnv
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 702: unable to resolve class Region
 @ line 702, column 14.
           List<Region> cnvAmplicons = this.amplicons[indices]
                ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 728: unable to resolve class Region
 @ line 728, column 34.
       Matrix getNormalisedCoverage(Region region, String sample) {
                                    ^

:compileGroovy FAILED
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 748: unable to resolve class Region
 @ line 748, column 34.
       def Matrix normaliseCoverage(Region region) {
                                    ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 765: unable to resolve class Region
 @ line 765, column 30.
       Matrix getCoverageMatrix(Region region) {
                                ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 779: unable to resolve class PileupIterator
 @ line 779, column 28.
               PileupIterator pileup
                              ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 782: unable to resolve class PileupIterator.Pileup
 @ line 782, column 48.
   ef sampleCov = pileup.collect { PileupIt
                                 ^


/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 816: unable to resolve class RangedData
FAILURE: Build failed with an exception.
 @ line 816, column 93.

   , Closure factory, Map<String,RangedData
* What went wrong:
                                 ^
Execution failed for task ':compileGroovy'.

> Compilation failed; see the compiler error output for details.
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 835: unable to resolve class Cli

 @ line 835, column 13.
* Try:
           Cli cli = new Cli(usage: "CNVDiagram <options>")
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
               ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 835: unable to resolve class Cli

 @ line 835, column 19.
BUILD FAILED
           Cli cli = new Cli(usage: "CNVDiagram <options>")

                     ^
Total time: 10.455 secs

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 875: unable to resolve class RangedData
 @ line 875, column 20.
           Map<String,RangedData> cnvCalls = [:]
                      ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 902: unable to resolve class BED
 @ line 902, column 27.
                   def bed = new BED(bedFile, withExtra:true).load()
                             ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 903: unable to resolve class Regions
 @ line 903, column 34.
                   cnvCalls[name] = new Regions()
                                    ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 936: unable to resolve class Regions
 @ line 936, column 17.
           Regions targetRegions = new BED(opts.targets).load().reduce()
                   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 936: unable to resolve class BED
 @ line 936, column 33.
           Regions targetRegions = new BED(opts.targets).load().reduce()
                                   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 976: unable to resolve class RefGenes
 @ line 976, column 30.
               diagram.geneDb = new RefGenes(opts.refseq, stripChr: cnvs.numberOfRanges>0 && !cnvs[0].chr.startsWith('chr'))
                                ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 980: unable to resolve class BED
 @ line 980, column 33.
               diagram.amplicons = new BED(opts.amplicons,withExtra:true).load()
                                   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1003: unable to resolve class Regions
 @ line 1003, column 5.
       private static Regions loadCNVs(OptionAccessor opts) {
       ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1004: unable to resolve class Regions
 @ line 1004, column 17.
           Regions cnvs
                   ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1010: unable to resolve class Region
 @ line 1010, column 20.
               Region cnv =  new Region(parts[2])
                      ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1010: unable to resolve class Region
 @ line 1010, column 27.
               Region cnv =  new Region(parts[2])
                             ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1014: unable to resolve class Regions
 @ line 1014, column 20.
               cnvs = new Regions()
                      ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1019: unable to resolve class Regions
 @ line 1019, column 20.
               cnvs = new Regions()
                      ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1020: unable to resolve class Region
 @ line 1020, column 60.
   , withExtra:true).load().each { Region r
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1020: unable to resolve class BED
 @ line 1020, column 13.
               new BED(opts.cnvs, withExtra:true).load().each { Region r ->
               ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1027: unable to resolve class RangedData
 @ line 1027, column 20.
               cnvs = new RangedData(opts.cnvs).load()
                      ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1030: unable to resolve class Regions
 @ line 1030, column 53.
   s.grep { it.chr == opts.chr } as Regions
                                 ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1036: unable to resolve class Regions
 @ line 1036, column 5.
       private Regions findLiteMeanRegions() {
       ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1040: unable to resolve class Regions
 @ line 1040, column 16.
          Regions result = new Regions()
                  ^

/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1040: unable to resolve class Regions
 @ line 1040, column 25.
          Regions result = new Regions()
                           ^

/home/sark/ximmer/src/main/groovy/CNVResults.groovy: 1: unable to resolve class gngs.RangedData
 @ line 1, column 1.
   import gngs.RangedData
   ^

/home/sark/ximmer/src/main/groovy/CNVResults.groovy: 27: unable to resolve class TargetedCNVAnnotator
 @ line 27, column 19.
       String toJson(TargetedCNVAnnotator annotator = null) {
                     ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 10: unable to resolve class htsjdk.samtools.SAMTagUtil
 @ line 10, column 1.
   import htsjdk.samtools.SAMTagUtil;
   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 8: unable to resolve class htsjdk.samtools.SAMFileWriter
 @ line 8, column 1.
   import htsjdk.samtools.SAMFileWriter;
   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 9: unable to resolve class htsjdk.samtools.SAMRecord
 @ line 9, column 1.
   import htsjdk.samtools.SAMRecord;
   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 38: unable to resolve class SAM
 @ line 38, column 5.
       SAM maleBam
       ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 40: unable to resolve class SAM
 @ line 40, column 5.
       SAM femaleBam
       ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 76: unable to resolve class DGV
 @ line 76, column 5.
       DGV dgv = null
       ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 90: unable to resolve class Regions
 @ line 90, column 5.
       private Regions targetRegions = null
       ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 99: unable to resolve class Regions
 @ line 99, column 25.
       public CNVSimulator(Regions targetRegions, String femaleBam, String maleBam) {
                           ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 100: unable to resolve class SAM
 @ line 100, column 29.
           this(targetRegions, new SAM(femaleBam), maleBam != null ? new SAM(maleBam) : null)
                               ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 100: unable to resolve class SAM
 @ line 100, column 67.
   femaleBam), maleBam != null ? new SAM(ma
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 103: unable to resolve class Regions
 @ line 103, column 25.
       public CNVSimulator(Regions targetRegions, SAM femaleBam, SAM maleBam) {
                           ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 103: unable to resolve class SAM
 @ line 103, column 48.
   ulator(Regions targetRegions, SAM female
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 103: unable to resolve class SAM
 @ line 103, column 63.
   targetRegions, SAM femaleBam, SAM maleBa
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 125: unable to resolve class Cli
 @ line 125, column 13.
           Cli cli = new Cli(usage:"CNVSimulator [options]")
               ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 125: unable to resolve class Cli
 @ line 125, column 19.
           Cli cli = new Cli(usage:"CNVSimulator [options]")
                     ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 155: unable to resolve class BED
 @ line 155, column 41.
     simulator.setTargetCoverage(new BED(op
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 168: unable to resolve class Region
 @ line 168, column 61.
   ts.o, new Regions().addRegion(new Region
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 168: unable to resolve class Regions
 @ line 168, column 37.
           simulator.createBam(opts.o, new Regions().addRegion(new Region(opts.region)))
                                       ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 172: unable to resolve class SAM
 @ line 172, column 28.
       int countAutosomeReads(SAM bam) {
                              ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 197: unable to resolve class Regions
 @ line 197, column 25.
                   Regions autosomalRegions = null
                           ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 206: unable to resolve class ProgressCounter
 @ line 206, column 33.
                   ProgressCounter counter = new ProgressCounter()
                                   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 206: unable to resolve class ProgressCounter
 @ line 206, column 43.
       ProgressCounter counter = new Progre
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 243: unable to resolve class Regions
 @ line 243, column 43.
   ateBam(String outputFileName, Regions re
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 270: unable to resolve class Regions
 @ line 270, column 39.
       List<SAMRecordPair> loadMaleReads(Regions cleanRegions) {
                                         ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 270: unable to resolve class SAMRecordPair
 @ line 270, column 10.
       List<SAMRecordPair> loadMaleReads(Regions cleanRegions) {
            ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 273: unable to resolve class SAMRecordPair
 @ line 273, column 14.
           List<SAMRecordPair> maleRegionReads = []
                ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 274: unable to resolve class Region
 @ line 274, column 9.
           for(Region cleanRegion in cleanRegions) {
           ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 276: unable to resolve class SAMRecordPair
 @ line 276, column 31.
                   SAMRecordPair pair = new SAMRecordPair(r1:r1,r2:r2)
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 276: unable to resolve class SAMRecordPair
 @ line 276, column 38.
                   SAMRecordPair pair = new SAMRecordPair(r1:r1,r2:r2)
                                        ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 286: unable to resolve class SAMRecordPair
 @ line 286, column 37.
           return maleRegionReads.sort { SAMRecordPair pair -> pair.r1.alignmentStart }
                                       ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 299: unable to resolve class Regions
 @ line 299, column 56.
   cement(String outputFileName, Regions cl
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 303: unable to resolve class SAMRecordPair
 @ line 303, column 14.
           List<SAMRecordPair> maleRegionReads = loadMaleReads(cleanRegions)
                ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 313: unable to resolve class ProgressCounter
 @ line 313, column 25.
           ProgressCounter writeProgress = new ProgressCounter()
                           ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 313: unable to resolve class ProgressCounter
 @ line 313, column 41.
   ogressCounter writeProgress = new Progre
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 318: unable to resolve class SAMRecordPair
 @ line 318, column 18.
           Iterator<SAMRecordPair> nextMaleRegionReadIterator = maleRegionReads.iterator()
                    ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 319: unable to resolve class SAMRecordPair
 @ line 319, column 23.
           SAMRecordPair nextMaleReadPair = nextMaleRegionReadIterator.next()
                         ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 321: unable to resolve class SAMRecordPair
 @ line 321, column 31.
           Closure setPairInfo = { SAMRecordPair pair ->
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 330: unable to resolve class SAMRecordPair
 @ line 330, column 34.
                      SAMRecordPair pair = nextMaleRegionReadIterator.next()
                                    ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 341: unable to resolve class SAMRecordPair
 @ line 341, column 96.
   : flushReads, spoolSize:8000) { SAMRecor
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 343: unable to resolve class SAMRecordPair
 @ line 343, column 18.
               List<SAMRecordPair> result = []
                    ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 364: unable to resolve class SAMRecordPair
 @ line 364, column 41.
   ordPair extractMaleReadsUntil(SAMRecordP
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 364: unable to resolve class SAMRecordPair
 @ line 364, column 71.
   SAMRecordPair start, Iterator<SAMRecordP
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 364: unable to resolve class SAMRecordPair
 @ line 364, column 92.
   Iterator<SAMRecordPair> iter, SAMRecordP
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 364: unable to resolve class SAMRecordPair
 @ line 364, column 117.
   ter, SAMRecordPair pair, List<SAMRecordP
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 363: unable to resolve class SAMRecordPair
 @ line 363, column 5.
       @CompileStatic
       ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 366: unable to resolve class SAMRecordPair
 @ line 366, column 22.
          SAMRecordPair nextMaleReadPair = start
                        ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 383: unable to resolve class Regions
 @ line 383, column 59.
   entOld(String outputFileName, Regions cl
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 387: unable to resolve class SAMRecordPair
 @ line 387, column 14.
           List<SAMRecordPair> maleRegionReads = loadMaleReads(cleanRegions)
                ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 398: unable to resolve class ProgressCounter
 @ line 398, column 25.
           ProgressCounter writeProgress = new ProgressCounter()
                           ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 398: unable to resolve class ProgressCouter
 @ line 398, column 41.
   ogressCounter writeProgress = new Progre
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 451: unable to resolve class SAMRecordPair
 @ line 451, column 26.
       boolean isPairBefore(SAMRecordPair pair1, SAMRecordPair pair2) {
                            ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 451: unable to resolve class SAMRecordPair
 @ line 451, column 47.
   irBefore(SAMRecordPair pair1, SAMRecordP
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 463: unable to resolve class Regions
 @ line 463, column 55.
   Sample(String outputFileName, Regions cl
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 478: unable to resolve class SAMRecordPair
 @ line 478, column 63.
   airs(options, outputFileName) { SAMRecor
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 532: unable to resolve class Regions
 @ line 532, column 28.
       Region findCleanRegion(Regions fromRegions, Region seedRegion) {
                              ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 532: unable to resolve class Region
 @ line 532, column 49.
   anRegion(Regions fromRegions, Region see
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 532: unable to resolve class Region
 @ line 532, column 5.
       Region findCleanRegion(Regions fromRegions, Region seedRegion) {
       ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 535: unable to resolve class Regions
 @ line 535, column 17.
           Regions seedWindow = fromRegions.window(seedRegion, 10).grep { it.chr == seedRegion.chr } as Regions
                   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 535: unable to resolve class Regions
 @ line 535, column 99.
    { it.chr == seedRegion.chr } as Regions
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 545: unable to resolve class Regions
 @ line 545, column 17.
           Regions maleReadRegions
                   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 547: unable to resolve class SAM
 @ line 547, column 17.
               SAM maleRegionBam = new SAM(maleBam.samFile)
                   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 547: unable to resolve class SAM
 @ line 547, column 33.
               SAM maleRegionBam = new SAM(maleBam.samFile)
                                   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 557: unable to resolve class Regions
 @ line 557, column 17.
           Regions femaleReadRegions = femaleBam.toPairRegions(chromosome,seedWindow[0].from,seedWindow[-1].to,500)
                   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 562: unable to resolve class Regions
 @ line 562, column 17.
           Regions combinedRegions = maleReadRegions ? maleReadRegions.reduce() : new Regions()
                   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 562: unable to resolve class Regions
 @ line 562, column 80.
    ? maleReadRegions.reduce() : new Region
                                 ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 572: unable to resolve class Regions
 @ line 572, column 21.
               Regions testRegions = femaleBam.toPairRegions(chromosome,seedWindow[0].from,seedWindow[-1].to,500)
                       ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 578: unable to resolve class Region
 @ line 578, column 16.
           Region result = new Region(chromosome, overlaps*.from.min()..overlaps*.to.max())
                  ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 578: unable to resolve class Region
 @ line 578, column 25.
           Region result = new Region(chromosome, overlaps*.from.min()..overlaps*.to.max())
                           ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 595: unable to resolve class Regions
 @ line 595, column 25.
       Region selectRegion(Regions fromRegions, int numRanges, Exclusions excludeRegions=null) {
                           ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 595: unable to resolve class Region
 @ line 595, column 5.
       Region selectRegion(Regions fromRegions, int numRanges, Exclusions excludeRegions=null) {
       ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 597: unable to resolve class Region
 @ line 597, column 16.
           Region cleanRegion  = null
                  ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 626: unable to resolve class Region
 @ line 626, column 20.
               Region seedRegion = new Region(chromosome,r)
                      ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 626: unable to resolve class Region
 @ line 626, column 33.
               Region seedRegion = new Region(chromosome,r)
                                   ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 633: unable to resolve class Region
 @ line 633, column 24.
                   Region candidateCleanRegion = findCleanRegion(fromRegions, seedRegion)
                          ^

/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 665: unable to resolve class Region
 @ line 665, column 40.
       boolean isOverlappingPopulationCNV(Region regionToCheck) {
                                          ^

/home/sark/ximmer/src/main/groovy/CodexResults.groovy: 5: unable to resolve class gngs.RangedData
 @ line 5, column 1.
   import gngs.RangedData
   ^

/home/sark/ximmer/src/main/groovy/CodexResults.groovy: 6: unable to resolve class gngs.Region
 @ line 6, column 1.
   import gngs.Region
   ^

/home/sark/ximmer/src/main/groovy/ConiferResults.groovy: 5: unable to resolve class gngs.RangedData
 @ line 5, column 1.
   import gngs.RangedData
   ^

/home/sark/ximmer/src/main/groovy/ConiferResults.groovy: 6: unable to resolve class gngs.Region
 @ line 6, column 1.
   import gngs.Region
   ^

/home/sark/ximmer/src/main/groovy/ExcavatorResults.groovy: 5: unable to resolve class gngs.RangedData
 @ line 5, column 1.
   import gngs.RangedData
   ^

/home/sark/ximmer/src/main/groovy/ExcavatorResults.groovy: 6: unable to resolve class gngs.Region
 @ line 6, column 1.
   import gngs.Region
   ^

/home/sark/ximmer/src/main/groovy/GATKMeanEstimator.groovy: 35: unable to resolve class GATKIntervalSummary
 @ line 35, column 33.
               GATKIntervalSummary summary = new GATKIntervalSummary(intervalFiles[sample].absolutePath)
                                   ^

/home/sark/ximmer/src/main/groovy/GATKMeanEstimator.groovy: 35: unable to resolve class GATKIntervalSummary
 @ line 35, column 43.
   GATKIntervalSummary summary = new GATKIn
                                 ^

/home/sark/ximmer/src/main/groovy/PositiveControlResults.groovy: 5: unable to resolve class gngs.RangedData
 @ line 5, column 1.
   import gngs.RangedData
   ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 8: unable to resolve class Cli
 @ line 8, column 5.
   Cli cli = new Cli(usage:"SimulateCNVs [options]\n")
       ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 8: unable to resolve class Cli
 @ line 8, column 11.
   Cli cli = new Cli(usage:"SimulateCNVs [options]\n")
             ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 50: unable to resolve class Pedigrees
 @ line 50, column 15.
       Pedigrees peds = Pedigrees.parse(opts.ped)
                 ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 60: unable to resolve class Regions
 @ line 60, column 9.
   Regions excludeRegions = null
           ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 62: unable to resolve class DGV
 @ line 62, column 9.
       DGV dgv = new DGV(opts.dgv).parse()
           ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 62: unable to resolve class DGV
 @ line 62, column 15.
       DGV dgv = new DGV(opts.dgv).parse()
                 ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 77: unable to resolve class Regions
 @ line 77, column 7.
       } as Regions
         ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 63: unable to resolve class Region
 @ line 63, column 31.
       excludeRegions = dgv.grep { Region cnv ->
                                 ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 99: unable to resolve class SAM
 @ line 99, column 12.
                bamFiles[new SAM(bam).samples[0]] = bam
              ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 124: unable to resolve class BED
 @ line 124, column 9.
       BED bed = new BED(opts.r).load()
           ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 124: unable to resolve class BED
 @ line 124, column 15.
       BED bed = new BED(opts.r).load()
                 ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 125: unable to resolve class Regions
 @ line 125, column 13.
       Regions coveredRegions = new BED(opts.abed).load().reduce()
               ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 125: unable to resolve class BED
 @ line 125, column 30.
       Regions coveredRegions = new BED(opts.abed).load().reduce()
                                ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 132: unable to resolve class Region
 @ line 132, column 12.
       Region r = simulator.selectRegion(bed, numRanges, excludeRegions)
              ^

/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 162: unable to resolve class SampleInfo
 @ line 162, column 13.
               new SampleInfo(sample: cnv.female, batch: new File(opts.d).name, target:"SIM", files: samples[cnv.female].files, sex: "FEMALE").toTsv()
               ^

/home/sark/ximmer/src/main/groovy/SimulationRun.groovy: 1: unable to resolve class gngs.SAM
 @ line 1, column 1.
   import gngs.SAM
   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 5: unable to resolve class graxxia.Stats
 @ line 5, column 1.
   import graxxia.Stats
   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 22: unable to resolve class RangedData
 @ line 22, column 16.
       Map<String,RangedData> results = [:]
                  ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 27: unable to resolve class Regions
 @ line 27, column 5.
       Regions targetRegions
       ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 37: unable to resolve class VCF
 @ line 37, column 10.
       List<VCF> vcfs = []
            ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 47: unable to resolve class Regions
 @ line 47, column 17.
       Map<String, Regions> variants = [:]
                   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 51: unable to resolve class TargetedCNVAnnotator
 @ line 51, column 5.
       TargetedCNVAnnotator cnvAnnotator = null
       ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 53: unable to resolve class RefGenes
 @ line 53, column 5.
       RefGenes refGenes = null
       ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 94: unable to resolve class RangedData
 @ line 94, column 93.
   , Closure factory, Map<String,RangedData
                                 ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 108: unable to resolve class Cli
 @ line 108, column 13.
           Cli cli = new Cli(usage: "SummarizeCNVs <options>")
               ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 108: unable to resolve class Cli
 @ line 108, column 19.
           Cli cli = new Cli(usage: "SummarizeCNVs <options>")
                     ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 151: unable to resolve class RangedData
 @ line 151, column 20.
           Map<String,RangedData> results = [:]
                      ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 198: unable to resolve class VCF
 @ line 198, column 14.
           List<VCF> vcfList = parseVCFs(opts, results)
                ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 200: unable to resolve class Regions
 @ line 200, column 17.
           Regions target = new BED(opts.target, withExtra:true).load()
                   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 200: unable to resolve class BED
 @ line 200, column 26.
           Regions target = new BED(opts.target, withExtra:true).load()
                            ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 206: unable to resolve class RefGenes
 @ line 206, column 22.
               RefGenes refGenes = (!opts.refgene || "download" == opts.refgene) ? RefGenes.download(opts.genome?:"hg19") : new RefGenes(opts.refgene)
                        ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 206: unable to resolve class RefGenes
 @ line 206, column 122.
   wnload(opts.genome?:"hg19") : new RefGen
                                 ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 227: unable to resolve class TargetedCNVAnnotator
 @ line 227, column 43.
       summarizer.cnvAnnotator = new Target
                                 ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 235: unable to resolve class RefGenes
 @ line 235, column 39.
                   summarizer.refGenes = new RefGenes(opts.refgene)
                                         ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 253: unable to resolve class Regions
 @ line 253, column 21.
               Regions cnvs = summarizer.run(exportSamples)
                       ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 302: unable to resolve class RangedData
 @ line 302, column 64.
   tionAccessor opts, Map<String,RangedData
                                 ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 302: unable to resolve class VCF
 @ line 302, column 17.
       static List<VCF> parseVCFs(OptionAccessor opts, Map<String,RangedData> results) {
                   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 303: unable to resolve class Regions
 @ line 303, column 17.
           Regions mergedCalls = results*.value.inject(new Regions()) { Regions regions, RangedData calls  ->
                   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 303: unable to resolve class Regions
 @ line 303, column 53.
   Calls = results*.value.inject(new Region
                                 ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 303: unable to resolve class Regions
 @ line 303, column 68.
   *.value.inject(new Regions()) { Regions
                                 ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 303: unable to resolve class RangedData
 @ line 303, column 68.
   *.value.inject(new Regions()) { Regions
                                 ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 308: unable to resolve class VCF
 @ line 308, column 14.
           List<VCF> vcfList = opts.vcfs ? opts.vcfs.collect {
                ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 309: unable to resolve class Variant
 @ line 309, column 27.
               VCF.parse(it) { Variant v ->
                             ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 329: unable to resolve class Regions
 @ line 329, column 5.
       Regions run(List exportSamples) {
       ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 335: unable to resolve class TargetedCNVAnnotator
 @ line 335, column 33.
               this.cnvAnnotator = new TargetedCNVAnnotator(targetRegions, dgvFile)
                                   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 347: unable to resolve class Regions
 @ line 347, column 17.
           Regions results = new Regions()
                   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 347: unable to resolve class Regions
 @ line 347, column 27.
           Regions results = new Regions()
                             ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 349: unable to resolve class Regions
 @ line 349, column 21.
               Regions sampleCnvs = extractSampleCnvs(s)
                       ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 383: unable to resolve class Regions
 @ line 383, column 23.
       void metaAnnotate(Regions results) {
                         ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 384: unable to resolve class Region
 @ line 384, column 9.
           for(Region cnv in results) {
           ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 394: unable to resolve class Regions
 @ line 394, column 19.
       void writeTSV(Regions cnvs, String fileName) {
                     ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 404: unable to resolve class Region
 @ line 404, column 39.
                   cnvAnnotator.annotate(new Region(cnv.chr, cnv.from..cnv.to), anno_types[cnv.type])
                                         ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 439: unable to resolve class Regions
 @ line 439, column 20.
       void writeJSON(Regions cnvs, String fileName) {
                      ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 449: unable to resolve class Region
 @ line 449, column 39.
                   cnvAnnotator.annotate(new Region(cnv.chr, cnv.from..cnv.to), anno_types[cnv.type])
                                         ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 496: unable to resolve class Regions
 @ line 496, column 22.
       void writeReport(Regions cnvs,
                        ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 574: unable to resolve class Regions
 @ line 574, column 5.
       Regions extractSampleCnvs(String sample) {
       ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 577: unable to resolve class Regions
 @ line 577, column 17.
           Regions merged = new Regions()
                   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 577: unable to resolve class Regions
 @ line 577, column 26.
           Regions merged = new Regions()
                            ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 579: unable to resolve class Region
 @ line 579, column 13.
               for(Region cnv in calls.grep { it.sample == sample }) {
               ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 584: unable to resolve class Regions
 @ line 584, column 17.
           Regions flattened = merged.reduce()
                   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 590: unable to resolve class Regions
 @ line 590, column 17.
           Regions result = new Regions()
                   ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 590: unable to resolve class Regions
 @ line 590, column 26.
           Regions result = new Regions()
                            ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 594: unable to resolve class Region
 @ line 594, column 9.
           for(Region cnv in flattened) {
           ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 603: unable to resolve class Region
 @ line 603, column 9.
           for(Region cnv in result) {
           ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 615: unable to resolve class Region
 @ line 615, column 46.
   iltered(List<String> callers, Region cnv
                                 ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 662: unable to resolve class Region
 @ line 662, column 26.
       def checkCallQuality(Region cnv, caller) {
                            ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 686: unable to resolve class Region
 @ line 686, column 51.
   (String sample, List callers, Region cnv
                                 ^

/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 691: unable to resolve class Region
 @ line 691, column 20.
               Region best = results[caller].grep { it.sample == sample && it.overlaps(cnv) }.max { it.quality?.toFloat() }
                      ^

/home/sark/ximmer/src/main/groovy/SummaryReport.groovy: 127: unable to resolve class Region
 @ line 127, column 14.
           List<Region> cnvs = ximmer.readCnvs()
                ^

/home/sark/ximmer/src/main/groovy/SummaryReport.groovy: 130: unable to resolve class RangedData
 @ line 130, column 14.
           List<RangedData> results = ximmer.runs*.value*.runDirectory.collect { runDir ->
                ^

/home/sark/ximmer/src/main/groovy/SummaryReport.groovy: 131: unable to resolve class RangedData
 @ line 131, column 13.
               new RangedData(new File(runDir,"$analysisCfg.analysisName/report/cnv_report.tsv").path).load([:], { r ->
               ^

/home/sark/ximmer/src/main/groovy/SummaryReport.groovy: 161: unable to resolve class Region
 @ line 161, column 37.
       void plotCNVSizeHistograms(List<Region> cnvs) {
                                       ^

/home/sark/ximmer/src/main/groovy/SummaryReport.groovy: 172: unable to resolve class Region
 @ line 172, column 36.
       File writeCombinedCNVInfo(List<Region> cnvs) {
                                      ^

/home/sark/ximmer/src/main/groovy/XHMMResults.groovy: 4: unable to resolve class gngs.RangedData
 @ line 4, column 1.
   import gngs.RangedData
   ^

/home/sark/ximmer/src/main/groovy/XHMMResults.groovy: 5: unable to resolve class gngs.Region
 @ line 5, column 1.
   import gngs.Region
   ^

/home/sark/ximmer/src/main/groovy/XHMMResults.groovy: 2: unable to resolve class com.xlson.groovycsv.PropertyMapper
 @ line 2, column 1.
   import com.xlson.groovycsv.PropertyMapper
   ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 72: unable to resolve class SAM
 @ line 72, column 17.
       Map<String, SAM> bamFiles = [:]
                   ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 74: unable to resolve class Pedigrees
 @ line 74, column 5.
       Pedigrees pedigrees = null
       ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 88: unable to resolve class Regions
 @ line 88, column 5.
       Regions targetRegion = null
       ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 90: unable to resolve class Regions
 @ line 90, column 5.
       Regions excludeRegions = null
       ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 100: unable to resolve class DGV
 @ line 100, column 5.
       DGV dgv
       ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 192: unable to resolve class BED
 @ line 192, column 29.
           this.targetRegion = new BED(cfg.target_regions).load().reduce()
                               ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 265: unable to resolve class DGV
 @ line 265, column 15.
           dgv = new DGV(dgvMergedFile.absolutePath).parse()
                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 655: unable to resolve class Pedigrees
 @ line 655, column 26.
           this.pedigrees = new Pedigrees()
                            ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 660: unable to resolve class Pedigrees
 @ line 660, column 23.
               Pedigrees males = Pedigrees.fromSingletons(cfg.samples.males)
                         ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 666: unable to resolve class Pedigrees
 @ line 666, column 23.
               Pedigrees females = Pedigrees.fromSingletons(cfg.samples.females)
                         ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 682: unable to resolve class SexKaryotyper
 @ line 682, column 14.
           List<SexKaryotyper> unknownResults = []
                ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 684: unable to resolve class SAM
 @ line 684, column 9.
           for(SAM sam in this.bamFiles*.value) {
           ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 686: unable to resolve class SexKaryotyper
 @ line 686, column 27.
               SexKaryotyper typer = new SexKaryotyper(sam, this.targetRegion)
                             ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 686: unable to resolve class SexKaryotyper
 @ line 686, column 35.
               SexKaryotyper typer = new SexKaryotyper(sam, this.targetRegion)
                                     ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 715: unable to resolve class Region
 @ line 715, column 10.
       List<Region> simulateRun(String runId) {
            ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 747: unable to resolve class SAM
 @ line 747, column 14.
           List<SAM> existingBams = Files.newDirectoryStream(bamDir.toPath(), '*.bam').grep { Path p ->
                ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 750: unable to resolve class SAM
 @ line 750, column 31.
           }.collect { Path p -> new SAM(p.toFile()) }
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 755: unable to resolve class SAM
 @ line 755, column 14.
           List<SAM> targetSamples = computeTargetSamples()
                ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 756: unable to resolve class Region
 @ line 756, column 14.
           List<Region> simulatedCNVs = []
                ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 759: unable to resolve class Regions
 @ line 759, column 17.
           Regions initialExclusions = this.excludeRegions ? this.excludeRegions.collect { it } as Regions : new Regions()
                   ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 759: unable to resolve class Regions
 @ line 759, column 94.
   excludeRegions.collect { it } as Regions
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 759: unable to resolve class Regions
 @ line 759, column 107.
   s.collect { it } as Regions : new Region
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 780: unable to resolve class Region
 @ line 780, column 47.
   VFile(File trueCnvsFile, List<Region> si
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 807: unable to resolve class RangedData
 @ line 807, column 20.
           RangedData cnvs = new RangedData(knownCnvsFile).load(columnNames: ['chr','start','end','sample','type'])
                      ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 807: unable to resolve class RangedData
 @ line 807, column 27.
           RangedData cnvs = new RangedData(knownCnvsFile).load(columnNames: ['chr','start','end','sample','type'])
                             ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 814: unable to resolve class SAM
 @ line 814, column 103.
   String> existingSamples, List<SAM> exist
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 814: unable to resolve class SAM
 @ line 814, column 122.
   ples, List<SAM> existingBams, SAM target
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 814: unable to resolve class Regions
 @ line 814, column 5.
       Regions simulateSampleCNVs(Exclusions exclusions, File bamDir, List<String> existingSamples, List<SAM> existingBams, SAM targetSAM) {
       ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 817: unable to resolve class Regions
 @ line 817, column 21.
               Regions cnvs = checkExistingSimulatedSample(bamDir, existingSamples, existingBams, sample)
                       ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 848: unable to resolve class Regions
 @ line 848, column 5.
       Regions checkExistingSimulatedSample(File outputDir, List existingSamples, List existingBams, String sample) {
       ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 855: unable to resolve class SAM
 @ line 855, column 13.
           SAM existingSAM = existingBams[existingIndex]
               ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 864: unable to resolve class Regions
 @ line 864, column 17.
           Regions result = new Regions()
                   ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 864: unable to resolve class Regions
 @ line 864, column 26.
           Regions result = new Regions()
                            ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 866: unable to resolve class Regions
 @ line 866, column 17.
           Regions cnvs = new BED(bedFile).load()
                   ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 866: unable to resolve class BED
 @ line 866, column 24.
           Regions cnvs = new BED(bedFile).load()
                          ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 881: unable to resolve class SAM
 @ line 881, column 71.
   s exclusions, File outputDir, SAM target
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 881: unable to resolve class Regions
 @ line 881, column 5.
       Regions simulateSampleCNVs(Exclusions exclusions, File outputDir, SAM targetSample) {
       ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 886: unable to resolve class SAM
 @ line 886, column 13.
           SAM sourceSample = null
               ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 899: unable to resolve class Regions
 @ line 899, column 17.
           Regions deletions = selectSampleCNVRegions(exclusions, targetSample, sourceSample)
                   ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 902: unable to resolve class Region
 @ line 902, column 16.
           Region r = deletions[0]
                  ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 940: unable to resolve class SAM
 @ line 940, column 59.
   egions(Exclusions exclusions, SAM target
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 940: unable to resolve class SAM
 @ line 940, column 77.
   exclusions, SAM targetSample, SAM source
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 940: unable to resolve class Regions
 @ line 940, column 5.
       Regions selectSampleCNVRegions(Exclusions exclusions, SAM targetSample, SAM sourceSample) {
       ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 944: unable to resolve class Regions
 @ line 944, column 17.
           Regions simulationRegions = this.targetRegion
                   ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 946: unable to resolve class Regions
 @ line 946, column 33.
               simulationRegions = new Regions(this.targetRegion.grep { it.chr == 'chrX' || it.chr == 'X' })
                                   ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 949: unable to resolve class Regions
 @ line 949, column 17.
           Regions deletions = new Regions()
                   ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 949: unable to resolve class Regions
 @ line 949, column 29.
           Regions deletions = new Regions()
                               ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 951: unable to resolve class Region
 @ line 951, column 20.
               Region r = selectSampleCNVRegion(exclusions, cnvIndex, simulationRegions, targetSample, sourceSample)
                      ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 960: unable to resolve class Regions
 @ line 960, column 68.
   usions exclusions, int cnvId, Regions si
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 960: unable to resolve class SAM
 @ line 960, column 95.
   d, Regions simulationRegions, SAM target
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 960: unable to resolve class SAM
 @ line 960, column 113.
   ionRegions, SAM targetSample, SAM source
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 960: unable to resolve class Region
 @ line 960, column 5.
       Region selectSampleCNVRegion(Exclusions exclusions, int cnvId, Regions simulationRegions, SAM targetSample, SAM sourceSample) {
       ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 977: unable to resolve class Region
 @ line 977, column 16.
           Region selectedRegion = Utils.withRetries(REGION_SIZE_SELECTION_RETRIES, message: "Select deletion region for $sampleId") {
                  ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 989: unable to resolve class Region
 @ line 989, column 20.
               Region r = simulator.selectRegion(simulationRegions, numRegions, exclusions)
                      ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1007: unable to resolve class SAM
 @ line 1007, column 10.
       List<SAM> computeTargetSamples() {
            ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1022: unable to resolve class SAM
 @ line 1022, column 18.
               List<SAM> results = this.bamFiles.grep { Map.Entry e ->
                    ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1078: unable to resolve class Region
 @ line 1078, column 10.
       List<Region> readCnvs() {
            ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1079: unable to resolve class Region
 @ line 1079, column 14.
           List<Region> cnvs = []
                ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1083: unable to resolve class Region
 @ line 1083, column 61.
   e,withExtra:true).load().each { Region r
                                 ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1083: unable to resolve class BED
 @ line 1083, column 17.
                   new BED(cnvFile,withExtra:true).load().each { Region r ->
                   ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1092: unable to resolve class Region
 @ line 1092, column 19.
           cnvs.each { Region r ->
                     ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1237: unable to resolve class Cli
 @ line 1237, column 13.
           Cli cli = new Cli(usage:"ximmer -c <config> -o <output_directory>")
               ^

/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1237: unable to resolve class Cli
 @ line 1237, column 19.
           Cli cli = new Cli(usage:"ximmer -c <config> -o <output_directory>")
                     ^

/home/sark/ximmer/src/main/groovy/ximmer/Exclusions.groovy: 5: unable to resolve class gngs.Region
 @ line 5, column 1.
   import gngs.Region
   ^

/home/sark/ximmer/src/main/groovy/ximmer/Exclusions.groovy: 6: unable to resolve class gngs.Regions
 @ line 6, column 1.
   import gngs.Regions
   ^

310 errors

@ssadedin
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I'm not sure if they are both related, but I think definitely your problems in the first case are because of some issues with capitalisation in the config.

  • cn.MOPs needs to be cnmops
  • Conifer needs to be conifer

Can you try fixing those, make sure you're updated to the latest code, and then see if the other issues are still occurring?

Thanks!

@SafinaAr
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Thank you. Do i need to download the ximmer again for the latest code?

@SafinaAr
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I'm now unable to reach that part of installation where i was earlier. I'm getting the following error:

Install directory detected as: /home/sark/ximmer

Error parsing 'bpipe.config' file. Cause: startup failed:
script15420974288811459166738.groovy: 43: illegal string body character after dollar sign;
   solution: either escape a literal dollar sign "\$5" or bracket the value expression "${5}" @ line 43, column 18.
            install = """
                    ^

1 error


=========================================== Bpipe Error ============================================

An error occurred executing your pipeline:

startup failed:
script15420974288811459166738.groovy: 43: illegal string body character after dollar sign;
   solution: either escape a literal dollar sign "\$5" or bracket the value expression "${5}" @ line 43, column 18.
            install = """
                    ^

1 error



Please see the details below for more information.

========================================== Error Details ===========================================

org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
script15420974288811459166738.groovy: 43: illegal string body character after dollar sign;
   solution: either escape a literal dollar sign "\$5" or bracket the value expression "${5}" @ line 43, column 18.
            install = """
                    ^

1 error

        at bpipe.Config$_readUserConfig_closure1$_closure4$_closure5.doCall(Config.groovy:156)
        at bpipe.Config$_readUserConfig_closure1$_closure4$_closure5.doCall(Config.groovy)
        at bpipe.Utils.time(Utils.groovy:674)
        at bpipe.Config$_readUserConfig_closure1$_closure4.doCall(Config.groovy:155)
        at groovyx.gpars.util.PAUtils$1.call(PAUtils.java:94)
        at groovyx.gpars.pa.ClosureMapper.op(ClosureMapper.java:36)
        at extra166y.AbstractParallelAnyArray$OOMPap.leafTransfer(AbstractParallelAnyArray.java:2249)
        at extra166y.PAS$FJOMap.atLeaf(PAS.java:228)
        at extra166y.PAS$FJBase.internalCompute(PAS.java:88)
        at extra166y.PAS$FJBase.compute(PAS.java:76)
        at jsr166y.RecursiveAction.exec(RecursiveAction.java:148)
        at jsr166y.ForkJoinTask.doExec(ForkJoinTask.java:305)
        at jsr166y.ForkJoinWorkerThread.execTask(ForkJoinWorkerThread.java:575)
        at jsr166y.ForkJoinPool.scan(ForkJoinPool.java:755)
        at jsr166y.ForkJoinPool.work(ForkJoinPool.java:617)
        at jsr166y.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:369)


====================================================================================================

More details about why this error occurred may be available in the full log file .bpipe/bpipe.log

@SafinaAr
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command.bpipe.log

@ssadedin
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Sorry for the slow response!

What's happening is that when you install it creates a bpipe.config file in eval/pipeline/bpipe.config. This seems to have gone wrong and produced a file that has invalid syntax. I'm very confused how it's gotten like that, but I wonder if you would mind attaching it to this issue or if that's not something you're comfortable, sending to me privately by email? There should not be anything sensitive in there, it is only setting the install directory I think.

@SafinaAr
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here is the file
bpipe.config.txt

Note:I have to change the extension of file to upload it here thast is why it is in txt format..

@ssadedin
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I think I may have fixed with my latest push - could you do git pull and try again?

Thanks!

@SafinaAr
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Hey thanks. I successfully installed ximmer and now running the ./ximmer script till now no error. Will update you if any occurs.

@SafinaAr
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Hi, Can you please tell me where i can find the .bpipe/bpipe.log file? As i have got errors.
Secondly can you please tell me how to change the directory for reference file?

@SafinaAr
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SafinaAr commented Nov 20, 2018 •
edited
Loading 

##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not read fasta file with exception /mnt/d/AKU/FTP/human_gnme_refrnces (Is a directory

These are the errors occurred for every bam file

@bopohdr
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bopohdr commented Nov 20, 2018

Secondly can you please tell me how to change the directory for reference file?

I provide path in config.groovy
HGFA="/Users/dmitrijsrots/Downloads/NGS_dati/reference/ucsc_hg19.fa"

@SafinaAr
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Hi ssadedin,
I ran:
./ximmer -v -nosim -c config.groovy -o test

My config.groovy:

HGFA="//mnt/d/AKU/FTP/human_gnme_refrnces/ucsc_hg19.fa"
bam_files="/mnt/d/AKU/FTP/BAMonly/*.bam"
target_regions="/mnt/d/AKU/FTP/BAM/TruSeq_exome_targeted_regions.hg19.bed"
concurrency=20
callers {
    cnmops {}
    exomedepth {}
        conifer {}
}

When i ran the above command im getting the following on the screen with errors:

Configured verbose logging
Ximmer  [1]     INFO    |7:01:00 Configured verbose logging
Ximmer  [1]     INFO    |7:01:00 Simulation disabled.
Ximmer  [1]     INFO    |7:01:00 No run directory configured: run directory = run
Ximmer  [1]     INFO    |7:01:00 Configuration validated!
SimulationRun   [1]     INFO    |7:01:16 Resolved BAM files for run 1: [/mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam, /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam, /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam]
SimulationRun   [1]     INFO    |7:01:17 Processing BAM Files:
/mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam
/mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam
/mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam
Ximmer  [1]     INFO    |7:01:17 Simulation disabled: analysis will be performed directly from source files
Ximmer  [1]     INFO    |7:01:17 No true positive CNVs configured for run 1
Ximmer  [1]     INFO    |7:01:17 Analysis has caller configuration: cnmops
Ximmer  [1]     INFO    |7:01:17 Anaysis keys are: []
Ximmer  [1]     INFO    |7:01:17 Write file test/run1/analysis/cnmops.default.params.txt with caller parameters
Ximmer  [1]     INFO    |7:01:17 Analysis has caller configuration: exomedepth
Ximmer  [1]     INFO    |7:01:17 Anaysis keys are: []
Ximmer  [1]     INFO    |7:01:17 Write file test/run1/analysis/ed.default.params.txt with caller parameters
Ximmer  [1]     INFO    |7:01:17 Analysis has caller configuration: conifer
Ximmer  [1]     INFO    |7:01:17 Anaysis keys are: []
Ximmer  [1]     INFO    |7:01:17 Write file test/run1/analysis/cfr.default.params.txt with caller parameters
Ximmer  [1]     INFO    |7:01:17 Executing Bpipe command: bash /home/sark/ximmer/bin/eval/bpipe run -n 20 -p TOOLS=/home/sark/ximmer/bin/eval/pipeline/tools -p DGV_CNVS=/home/sark/ximmer/bin/cache/dgvMerged.txt.gz -p XIMMER_SRC=/home/sark/ximmer/bin/src/main/groovy -p callers=cnmops,ed,cfr -p refgene=/home/sark/ximmer/bin/cache/refGene.txt.gz -p simulation=false -p batches=analysis -p target_bed=/mnt/d/AKU/FTP/BAM/TruSeq_exome_targeted_regions.hg19.bed -p sample_id_mask="" -p imgpath=run1/#batch#/report/ /home/sark/ximmer/bin/eval/pipeline/exome_cnv_pipeline.groovy /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam
====================================================================================================

  | |/ /(_)___ ___  ____ ___  ___  _____
  |   // / __ `__ \/ __ `__ \/ _ \/ ___/
 /   |/ / / / / / / / / / / /  __/ /
/_/|_/_/_/ /_/ /_/_/ /_/ /_/\___/_/

Ximmer Integrated CNV Analysis Pipeline

====================================================================================================
Scanning target region ...
Chromosomes for analysis are: [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX]
====================================================================================================
|                              Starting Pipeline at 2018-11-22 07:01                               |
====================================================================================================

============================================ Stage init ============================================

================================== Stage create_analysable_target ==================================

====================================== Stage init_common (1) =======================================
Running Common Stages

=========================== Stage gatk_depth_of_coverage (m11.germline) ============================

=========================== Stage gatk_depth_of_coverage (m12.germline) ============================

============================= Stage gatk_depth_of_coverage (m12.tumor) =============================

============================= Stage gatk_depth_of_coverage (m11.tumor) =============================

============================= Stage gatk_depth_of_coverage (m14.tumor) =============================

=========================== Stage gatk_depth_of_coverage (m14.germline) ============================
INFO  07:01:38,728 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:38,760 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:38,760 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:38,760 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:38,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:38,763 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m12.germline.recal
INFO  07:01:38,764 HelpFormatter - Date/Time: 2018/11/22 07:01:38
INFO  07:01:38,764 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:38,764 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:38,799 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:38,807 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:39,421 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:39,442 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,442 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:39,442 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:39,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:39,446 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m11.tumor.recal
INFO  07:01:39,447 HelpFormatter - Date/Time: 2018/11/22 07:01:39
INFO  07:01:39,447 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,447 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,455 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:39,459 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:39,423 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:39,446 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:39,447 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:39,447 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:39,451 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m12.tumor.recal
INFO  07:01:39,452 HelpFormatter - Date/Time: 2018/11/22 07:01:39
INFO  07:01:39,452 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,452 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,460 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:39,464 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:40,243 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:40,259 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,260 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:40,260 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:40,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:40,263 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m14.tumor.recal
INFO  07:01:40,263 HelpFormatter - Date/Time: 2018/11/22 07:01:40
INFO  07:01:40,263 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,263 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,270 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:40,273 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:40,739 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:40,761 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,761 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:40,761 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:40,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:40,765 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m11.germline.recal
INFO  07:01:40,766 HelpFormatter - Date/Time: 2018/11/22 07:01:40
INFO  07:01:40,766 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,766 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,774 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:40,779 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:40,720 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:40,736 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,737 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:40,737 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:40,737 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:40,740 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m14.germline.recal
INFO  07:01:40,740 HelpFormatter - Date/Time: 2018/11/22 07:01:40
INFO  07:01:40,740 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,740 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,748 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:40,752 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
WARN  07:01:42,011 RestStorageService - Error Response: PUT '/GATK_Run_Reports/JVidf16r7L24s7pFTqtMOuKZxQ1BgEhf.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 813, x-amz-meta-md5-hash: 167717ea61777222cce66c1a50bb99cb, Content-Type: application/octet-stream, Content-MD5: FncX6mF3ciLM5mwaULuZyw==, Date: Thu, 22 Nov 2018 07:01:40 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:W/TCv3aq1iKBF/5v0phsrDtVLgE=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 3F75C411187EF113, x-amz-id-2: xnFFPAR6fRUriAxd8EM8E/EIsiFgF9NUngM3shVw1MJbtRKtxIQMd2zAqLkK6c4HcFYoaNT77xE=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
WARN  07:01:41,613 RestStorageService - Error Response: PUT '/GATK_Run_Reports/yDQecrcM5bRb6GhzgcYhzCfem9TNj941.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 812, x-amz-meta-md5-hash: d022601a3f56b72ee76979cdfcc6e5a0, Content-Type: application/octet-stream, Content-MD5: 0CJgGj9Wty7naXnN/MbloA==, Date: Thu, 22 Nov 2018 07:01:39 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:Hwzi7pR8Zy1ZRFkowJ+TpecqdqA=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 3C57374BC34CBD92, x-amz-id-2: rgXiTycpWYH+8SX/bEwsJMM/iUT+z9h3OnLqMWz91olwBe5n5qwWf7tUHvdA21CWBSoc4gAIgHQ=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,599 RestStorageService - Error Response: PUT '/GATK_Run_Reports/IojLAXcx2m6C3adRYD4zSB7V6hGeUfo3.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 812, x-amz-meta-md5-hash: c588b122161c7da28b80c24af1c88279, Content-Type: application/octet-stream, Content-MD5: xYixIhYcfaKLgMJK8ciCeQ==, Date: Thu, 22 Nov 2018 07:01:40 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:r7HQMTprAdg7uN9/2lC1eyhiXJ8=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: CC515BCC13D62DE8, x-amz-id-2: Ex++Xhklq29+r/K78OkR1yzkQrKJu1EE0ZS7sxpyOg7OzIXB8V0lRzgp/QJuLnU6Ua+jGXrxh9U=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,594 RestStorageService - Error Response: PUT '/GATK_Run_Reports/YZdfTTtcLqwbFZWMDuxsPp4MNeCkCvhh.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 814, x-amz-meta-md5-hash: 11e1fa5c716365dc62c3f94fb20acdc7, Content-Type: application/octet-stream, Content-MD5: EeH6XHFjZdxiw/lPsgrNxw==, Date: Thu, 22 Nov 2018 07:01:39 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:C8/U35TQhmIGCNJcViHM/nisq9w=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 8B1D7731D8207E18, x-amz-id-2: /wHRXek3OKxp48f0oSg1T4+sT8LnrwKNGX03ATPosjAL7z1VKL62Vwa+1LR1bsAZQiyMJ2osVuk=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,759 RestStorageService - Error Response: PUT '/GATK_Run_Reports/TCyEkthDoRUlWtNTby5RVxxJBnlOkllB.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 812, x-amz-meta-md5-hash: 83deffc1546e1ce1c47f08b19c1d6625, Content-Type: application/octet-stream, Content-MD5: g97/wVRuHOHEfwixnB1mJQ==, Date: Thu, 22 Nov 2018 07:01:39 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:18QRW7NJk5Aw+dKHuOYqisInd1c=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 65C41E369B0BEF3C, x-amz-id-2: 4mcaOjizm4X5Xy2c+oDLe4yEhSMfrjnWjg42rGo4hTtWBucfsKg+d45sZ1IL5/4/wN0G7+fOhv8=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,993 RestStorageService - Error Response: PUT '/GATK_Run_Reports/HaxgwTmtdmBIlUotyoHkCj8zIRYJi4Yt.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 813, x-amz-meta-md5-hash: 72aa2bfd9de4bb28b9898c8353b8ef1a, Content-Type: application/octet-stream, Content-MD5: cqor/Z3kuyi5iYyDU7jvGg==, Date: Thu, 22 Nov 2018 07:01:40 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:lA3pFlMUKZH88f8ayWzT0JIXvYQ=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 44FEA86274ED883A, x-amz-id-2: 0X1PqJXKPnq4/arw/8lSEVU4C65clUNDTQSXhlzFwO5EA7HBHy5dwZSPd2A6TVRBdUvYbmLQXo0=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.germline.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.tumor.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.germline.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.tumor.recal

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.tumor.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.germline.recal


========================================= Pipeline Failed ==========================================

One or more parallel stages aborted. The following messages were reported:

--------------------------- gatk_depth_of_coverage  ( m14.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.tumor.recal

--------------------------- gatk_depth_of_coverage  ( m11.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.tumor.recal

------------------------- gatk_depth_of_coverage  ( m14.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.germline.recal

------------------------- gatk_depth_of_coverage  ( m11.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.germline.recal

------------------------- gatk_depth_of_coverage  ( m12.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.germline.recal

--------------------------- gatk_depth_of_coverage  ( m12.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.tumor.recal

----------------------------------------------------------------------------------------------------

Use 'bpipe errors' to see output from failed commands.


Caught: java.lang.RuntimeException: Analysis failed for test/run1:
java.lang.RuntimeException: Analysis failed for test/run1:
        at Ximmer.runAnalysisForRun(Ximmer.groovy:462)
        at Ximmer$runAnalysisForRun$2.callCurrent(Unknown Source)
        at Ximmer.runAnalysis(Ximmer.groovy:337)
        at Ximmer$runAnalysis$1.callCurrent(Unknown Source)
        at Ximmer.run(Ximmer.groovy:199)
        at Ximmer$run.call(Unknown Source)
        at Ximmer.main(Ximmer.groovy:1279)

Can you please help me with this?

@bopohdr
Copy link

bopohdr commented Nov 22, 2018

Hi ssadedin,
I ran:
./ximmer -v -nosim -c config.groovy -o test

My config.groovy:

HGFA="//mnt/d/AKU/FTP/human_gnme_refrnces/ucsc_hg19.fa"
bam_files="/mnt/d/AKU/FTP/BAMonly/*.bam"
target_regions="/mnt/d/AKU/FTP/BAM/TruSeq_exome_targeted_regions.hg19.bed"
concurrency=20
callers {
    cnmops {}
    exomedepth {}
        conifer {}
}

When i ran the above command im getting the following on the screen with errors:

Configured verbose logging
Ximmer  [1]     INFO    |7:01:00 Configured verbose logging
Ximmer  [1]     INFO    |7:01:00 Simulation disabled.
Ximmer  [1]     INFO    |7:01:00 No run directory configured: run directory = run
Ximmer  [1]     INFO    |7:01:00 Configuration validated!
SimulationRun   [1]     INFO    |7:01:16 Resolved BAM files for run 1: [/mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam, /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam, /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam]
SimulationRun   [1]     INFO    |7:01:17 Processing BAM Files:
/mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam
/mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam
/mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam
Ximmer  [1]     INFO    |7:01:17 Simulation disabled: analysis will be performed directly from source files
Ximmer  [1]     INFO    |7:01:17 No true positive CNVs configured for run 1
Ximmer  [1]     INFO    |7:01:17 Analysis has caller configuration: cnmops
Ximmer  [1]     INFO    |7:01:17 Anaysis keys are: []
Ximmer  [1]     INFO    |7:01:17 Write file test/run1/analysis/cnmops.default.params.txt with caller parameters
Ximmer  [1]     INFO    |7:01:17 Analysis has caller configuration: exomedepth
Ximmer  [1]     INFO    |7:01:17 Anaysis keys are: []
Ximmer  [1]     INFO    |7:01:17 Write file test/run1/analysis/ed.default.params.txt with caller parameters
Ximmer  [1]     INFO    |7:01:17 Analysis has caller configuration: conifer
Ximmer  [1]     INFO    |7:01:17 Anaysis keys are: []
Ximmer  [1]     INFO    |7:01:17 Write file test/run1/analysis/cfr.default.params.txt with caller parameters
Ximmer  [1]     INFO    |7:01:17 Executing Bpipe command: bash /home/sark/ximmer/bin/eval/bpipe run -n 20 -p TOOLS=/home/sark/ximmer/bin/eval/pipeline/tools -p DGV_CNVS=/home/sark/ximmer/bin/cache/dgvMerged.txt.gz -p XIMMER_SRC=/home/sark/ximmer/bin/src/main/groovy -p callers=cnmops,ed,cfr -p refgene=/home/sark/ximmer/bin/cache/refGene.txt.gz -p simulation=false -p batches=analysis -p target_bed=/mnt/d/AKU/FTP/BAM/TruSeq_exome_targeted_regions.hg19.bed -p sample_id_mask="" -p imgpath=run1/#batch#/report/ /home/sark/ximmer/bin/eval/pipeline/exome_cnv_pipeline.groovy /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam
====================================================================================================

  | |/ /(_)___ ___  ____ ___  ___  _____
  |   // / __ `__ \/ __ `__ \/ _ \/ ___/
 /   |/ / / / / / / / / / / /  __/ /
/_/|_/_/_/ /_/ /_/_/ /_/ /_/\___/_/

Ximmer Integrated CNV Analysis Pipeline

====================================================================================================
Scanning target region ...
Chromosomes for analysis are: [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX]
====================================================================================================
|                              Starting Pipeline at 2018-11-22 07:01                               |
====================================================================================================

============================================ Stage init ============================================

================================== Stage create_analysable_target ==================================

====================================== Stage init_common (1) =======================================
Running Common Stages

=========================== Stage gatk_depth_of_coverage (m11.germline) ============================

=========================== Stage gatk_depth_of_coverage (m12.germline) ============================

============================= Stage gatk_depth_of_coverage (m12.tumor) =============================

============================= Stage gatk_depth_of_coverage (m11.tumor) =============================

============================= Stage gatk_depth_of_coverage (m14.tumor) =============================

=========================== Stage gatk_depth_of_coverage (m14.germline) ============================
INFO  07:01:38,728 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:38,760 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:38,760 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:38,760 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:38,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:38,763 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m12.germline.recal
INFO  07:01:38,764 HelpFormatter - Date/Time: 2018/11/22 07:01:38
INFO  07:01:38,764 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:38,764 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:38,799 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:38,807 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:39,421 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:39,442 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,442 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:39,442 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:39,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:39,446 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m11.tumor.recal
INFO  07:01:39,447 HelpFormatter - Date/Time: 2018/11/22 07:01:39
INFO  07:01:39,447 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,447 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,455 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:39,459 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:39,423 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:39,446 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:39,447 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:39,447 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:39,451 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m12.tumor.recal
INFO  07:01:39,452 HelpFormatter - Date/Time: 2018/11/22 07:01:39
INFO  07:01:39,452 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,452 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,460 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:39,464 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:40,243 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:40,259 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,260 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:40,260 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:40,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:40,263 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m14.tumor.recal
INFO  07:01:40,263 HelpFormatter - Date/Time: 2018/11/22 07:01:40
INFO  07:01:40,263 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,263 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,270 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:40,273 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:40,739 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:40,761 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,761 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:40,761 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:40,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:40,765 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m11.germline.recal
INFO  07:01:40,766 HelpFormatter - Date/Time: 2018/11/22 07:01:40
INFO  07:01:40,766 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,766 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,774 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:40,779 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:40,720 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:40,736 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,737 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:40,737 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:40,737 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:40,740 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m14.germline.recal
INFO  07:01:40,740 HelpFormatter - Date/Time: 2018/11/22 07:01:40
INFO  07:01:40,740 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,740 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,748 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:40,752 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
WARN  07:01:42,011 RestStorageService - Error Response: PUT '/GATK_Run_Reports/JVidf16r7L24s7pFTqtMOuKZxQ1BgEhf.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 813, x-amz-meta-md5-hash: 167717ea61777222cce66c1a50bb99cb, Content-Type: application/octet-stream, Content-MD5: FncX6mF3ciLM5mwaULuZyw==, Date: Thu, 22 Nov 2018 07:01:40 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:W/TCv3aq1iKBF/5v0phsrDtVLgE=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 3F75C411187EF113, x-amz-id-2: xnFFPAR6fRUriAxd8EM8E/EIsiFgF9NUngM3shVw1MJbtRKtxIQMd2zAqLkK6c4HcFYoaNT77xE=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
WARN  07:01:41,613 RestStorageService - Error Response: PUT '/GATK_Run_Reports/yDQecrcM5bRb6GhzgcYhzCfem9TNj941.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 812, x-amz-meta-md5-hash: d022601a3f56b72ee76979cdfcc6e5a0, Content-Type: application/octet-stream, Content-MD5: 0CJgGj9Wty7naXnN/MbloA==, Date: Thu, 22 Nov 2018 07:01:39 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:Hwzi7pR8Zy1ZRFkowJ+TpecqdqA=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 3C57374BC34CBD92, x-amz-id-2: rgXiTycpWYH+8SX/bEwsJMM/iUT+z9h3OnLqMWz91olwBe5n5qwWf7tUHvdA21CWBSoc4gAIgHQ=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,599 RestStorageService - Error Response: PUT '/GATK_Run_Reports/IojLAXcx2m6C3adRYD4zSB7V6hGeUfo3.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 812, x-amz-meta-md5-hash: c588b122161c7da28b80c24af1c88279, Content-Type: application/octet-stream, Content-MD5: xYixIhYcfaKLgMJK8ciCeQ==, Date: Thu, 22 Nov 2018 07:01:40 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:r7HQMTprAdg7uN9/2lC1eyhiXJ8=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: CC515BCC13D62DE8, x-amz-id-2: Ex++Xhklq29+r/K78OkR1yzkQrKJu1EE0ZS7sxpyOg7OzIXB8V0lRzgp/QJuLnU6Ua+jGXrxh9U=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,594 RestStorageService - Error Response: PUT '/GATK_Run_Reports/YZdfTTtcLqwbFZWMDuxsPp4MNeCkCvhh.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 814, x-amz-meta-md5-hash: 11e1fa5c716365dc62c3f94fb20acdc7, Content-Type: application/octet-stream, Content-MD5: EeH6XHFjZdxiw/lPsgrNxw==, Date: Thu, 22 Nov 2018 07:01:39 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:C8/U35TQhmIGCNJcViHM/nisq9w=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 8B1D7731D8207E18, x-amz-id-2: /wHRXek3OKxp48f0oSg1T4+sT8LnrwKNGX03ATPosjAL7z1VKL62Vwa+1LR1bsAZQiyMJ2osVuk=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,759 RestStorageService - Error Response: PUT '/GATK_Run_Reports/TCyEkthDoRUlWtNTby5RVxxJBnlOkllB.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 812, x-amz-meta-md5-hash: 83deffc1546e1ce1c47f08b19c1d6625, Content-Type: application/octet-stream, Content-MD5: g97/wVRuHOHEfwixnB1mJQ==, Date: Thu, 22 Nov 2018 07:01:39 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:18QRW7NJk5Aw+dKHuOYqisInd1c=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 65C41E369B0BEF3C, x-amz-id-2: 4mcaOjizm4X5Xy2c+oDLe4yEhSMfrjnWjg42rGo4hTtWBucfsKg+d45sZ1IL5/4/wN0G7+fOhv8=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,993 RestStorageService - Error Response: PUT '/GATK_Run_Reports/HaxgwTmtdmBIlUotyoHkCj8zIRYJi4Yt.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 813, x-amz-meta-md5-hash: 72aa2bfd9de4bb28b9898c8353b8ef1a, Content-Type: application/octet-stream, Content-MD5: cqor/Z3kuyi5iYyDU7jvGg==, Date: Thu, 22 Nov 2018 07:01:40 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:lA3pFlMUKZH88f8ayWzT0JIXvYQ=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 44FEA86274ED883A, x-amz-id-2: 0X1PqJXKPnq4/arw/8lSEVU4C65clUNDTQSXhlzFwO5EA7HBHy5dwZSPd2A6TVRBdUvYbmLQXo0=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.germline.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.tumor.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.germline.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.tumor.recal

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.tumor.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.germline.recal


========================================= Pipeline Failed ==========================================

One or more parallel stages aborted. The following messages were reported:

--------------------------- gatk_depth_of_coverage  ( m14.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.tumor.recal

--------------------------- gatk_depth_of_coverage  ( m11.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.tumor.recal

------------------------- gatk_depth_of_coverage  ( m14.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.germline.recal

------------------------- gatk_depth_of_coverage  ( m11.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.germline.recal

------------------------- gatk_depth_of_coverage  ( m12.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.germline.recal

--------------------------- gatk_depth_of_coverage  ( m12.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.tumor.recal

----------------------------------------------------------------------------------------------------

Use 'bpipe errors' to see output from failed commands.


Caught: java.lang.RuntimeException: Analysis failed for test/run1:
java.lang.RuntimeException: Analysis failed for test/run1:
        at Ximmer.runAnalysisForRun(Ximmer.groovy:462)
        at Ximmer$runAnalysisForRun$2.callCurrent(Unknown Source)
        at Ximmer.runAnalysis(Ximmer.groovy:337)
        at Ximmer$runAnalysis$1.callCurrent(Unknown Source)
        at Ximmer.run(Ximmer.groovy:199)
        at Ximmer$run.call(Unknown Source)
        at Ximmer.main(Ximmer.groovy:1279)

Can you please help me with this?

Does it happen with all callers ? Try to switch them one by one in config.qroovy (my ximmer installation unable to run Codex and Conifer, but other are ok).

Does Your reference file contain also index .fa.fai and fa.dict in the same folder ?

@SafinaAr
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Author

Hi ssadedin,
I ran:
./ximmer -v -nosim -c config.groovy -o test
My config.groovy:

HGFA="//mnt/d/AKU/FTP/human_gnme_refrnces/ucsc_hg19.fa"
bam_files="/mnt/d/AKU/FTP/BAMonly/*.bam"
target_regions="/mnt/d/AKU/FTP/BAM/TruSeq_exome_targeted_regions.hg19.bed"
concurrency=20
callers {
    cnmops {}
    exomedepth {}
        conifer {}
}

When i ran the above command im getting the following on the screen with errors:

Configured verbose logging
Ximmer  [1]     INFO    |7:01:00 Configured verbose logging
Ximmer  [1]     INFO    |7:01:00 Simulation disabled.
Ximmer  [1]     INFO    |7:01:00 No run directory configured: run directory = run
Ximmer  [1]     INFO    |7:01:00 Configuration validated!
SimulationRun   [1]     INFO    |7:01:16 Resolved BAM files for run 1: [/mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam, /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam, /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam]
SimulationRun   [1]     INFO    |7:01:17 Processing BAM Files:
/mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam
/mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam
/mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam
Ximmer  [1]     INFO    |7:01:17 Simulation disabled: analysis will be performed directly from source files
Ximmer  [1]     INFO    |7:01:17 No true positive CNVs configured for run 1
Ximmer  [1]     INFO    |7:01:17 Analysis has caller configuration: cnmops
Ximmer  [1]     INFO    |7:01:17 Anaysis keys are: []
Ximmer  [1]     INFO    |7:01:17 Write file test/run1/analysis/cnmops.default.params.txt with caller parameters
Ximmer  [1]     INFO    |7:01:17 Analysis has caller configuration: exomedepth
Ximmer  [1]     INFO    |7:01:17 Anaysis keys are: []
Ximmer  [1]     INFO    |7:01:17 Write file test/run1/analysis/ed.default.params.txt with caller parameters
Ximmer  [1]     INFO    |7:01:17 Analysis has caller configuration: conifer
Ximmer  [1]     INFO    |7:01:17 Anaysis keys are: []
Ximmer  [1]     INFO    |7:01:17 Write file test/run1/analysis/cfr.default.params.txt with caller parameters
Ximmer  [1]     INFO    |7:01:17 Executing Bpipe command: bash /home/sark/ximmer/bin/eval/bpipe run -n 20 -p TOOLS=/home/sark/ximmer/bin/eval/pipeline/tools -p DGV_CNVS=/home/sark/ximmer/bin/cache/dgvMerged.txt.gz -p XIMMER_SRC=/home/sark/ximmer/bin/src/main/groovy -p callers=cnmops,ed,cfr -p refgene=/home/sark/ximmer/bin/cache/refGene.txt.gz -p simulation=false -p batches=analysis -p target_bed=/mnt/d/AKU/FTP/BAM/TruSeq_exome_targeted_regions.hg19.bed -p sample_id_mask="" -p imgpath=run1/#batch#/report/ /home/sark/ximmer/bin/eval/pipeline/exome_cnv_pipeline.groovy /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam
====================================================================================================

  | |/ /(_)___ ___  ____ ___  ___  _____
  |   // / __ `__ \/ __ `__ \/ _ \/ ___/
 /   |/ / / / / / / / / / / /  __/ /
/_/|_/_/_/ /_/ /_/_/ /_/ /_/\___/_/

Ximmer Integrated CNV Analysis Pipeline

====================================================================================================
Scanning target region ...
Chromosomes for analysis are: [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX]
====================================================================================================
|                              Starting Pipeline at 2018-11-22 07:01                               |
====================================================================================================

============================================ Stage init ============================================

================================== Stage create_analysable_target ==================================

====================================== Stage init_common (1) =======================================
Running Common Stages

=========================== Stage gatk_depth_of_coverage (m11.germline) ============================

=========================== Stage gatk_depth_of_coverage (m12.germline) ============================

============================= Stage gatk_depth_of_coverage (m12.tumor) =============================

============================= Stage gatk_depth_of_coverage (m11.tumor) =============================

============================= Stage gatk_depth_of_coverage (m14.tumor) =============================

=========================== Stage gatk_depth_of_coverage (m14.germline) ============================
INFO  07:01:38,728 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:38,760 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:38,760 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:38,760 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:38,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:38,763 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m12.germline.recal
INFO  07:01:38,764 HelpFormatter - Date/Time: 2018/11/22 07:01:38
INFO  07:01:38,764 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:38,764 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:38,799 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:38,807 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:39,421 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:39,442 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,442 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:39,442 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:39,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:39,446 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m11.tumor.recal
INFO  07:01:39,447 HelpFormatter - Date/Time: 2018/11/22 07:01:39
INFO  07:01:39,447 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,447 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,455 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:39,459 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:39,423 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:39,446 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:39,447 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:39,447 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:39,451 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m12.tumor.recal
INFO  07:01:39,452 HelpFormatter - Date/Time: 2018/11/22 07:01:39
INFO  07:01:39,452 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,452 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:39,460 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:39,464 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:40,243 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:40,259 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,260 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:40,260 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:40,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:40,263 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m14.tumor.recal
INFO  07:01:40,263 HelpFormatter - Date/Time: 2018/11/22 07:01:40
INFO  07:01:40,263 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,263 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,270 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:40,273 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:40,739 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:40,761 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,761 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:40,761 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:40,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:40,765 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m11.germline.recal
INFO  07:01:40,766 HelpFormatter - Date/Time: 2018/11/22 07:01:40
INFO  07:01:40,766 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,766 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,774 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:40,779 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
INFO  07:01:40,720 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  07:01:40,736 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,737 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  07:01:40,737 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  07:01:40,737 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  07:01:40,740 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m14.germline.recal
INFO  07:01:40,740 HelpFormatter - Date/Time: 2018/11/22 07:01:40
INFO  07:01:40,740 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,740 HelpFormatter - --------------------------------------------------------------------------------
INFO  07:01:40,748 GenomeAnalysisEngine - Strictness is SILENT
WARN  07:01:40,752 FSLockWithShared - WARNING: Unable to lock file /mnt/d/AKU/FTP/human_gnme_refrnces (could not open read only file channel)
WARN  07:01:42,011 RestStorageService - Error Response: PUT '/GATK_Run_Reports/JVidf16r7L24s7pFTqtMOuKZxQ1BgEhf.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 813, x-amz-meta-md5-hash: 167717ea61777222cce66c1a50bb99cb, Content-Type: application/octet-stream, Content-MD5: FncX6mF3ciLM5mwaULuZyw==, Date: Thu, 22 Nov 2018 07:01:40 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:W/TCv3aq1iKBF/5v0phsrDtVLgE=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 3F75C411187EF113, x-amz-id-2: xnFFPAR6fRUriAxd8EM8E/EIsiFgF9NUngM3shVw1MJbtRKtxIQMd2zAqLkK6c4HcFYoaNT77xE=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
WARN  07:01:41,613 RestStorageService - Error Response: PUT '/GATK_Run_Reports/yDQecrcM5bRb6GhzgcYhzCfem9TNj941.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 812, x-amz-meta-md5-hash: d022601a3f56b72ee76979cdfcc6e5a0, Content-Type: application/octet-stream, Content-MD5: 0CJgGj9Wty7naXnN/MbloA==, Date: Thu, 22 Nov 2018 07:01:39 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:Hwzi7pR8Zy1ZRFkowJ+TpecqdqA=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 3C57374BC34CBD92, x-amz-id-2: rgXiTycpWYH+8SX/bEwsJMM/iUT+z9h3OnLqMWz91olwBe5n5qwWf7tUHvdA21CWBSoc4gAIgHQ=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,599 RestStorageService - Error Response: PUT '/GATK_Run_Reports/IojLAXcx2m6C3adRYD4zSB7V6hGeUfo3.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 812, x-amz-meta-md5-hash: c588b122161c7da28b80c24af1c88279, Content-Type: application/octet-stream, Content-MD5: xYixIhYcfaKLgMJK8ciCeQ==, Date: Thu, 22 Nov 2018 07:01:40 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:r7HQMTprAdg7uN9/2lC1eyhiXJ8=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: CC515BCC13D62DE8, x-amz-id-2: Ex++Xhklq29+r/K78OkR1yzkQrKJu1EE0ZS7sxpyOg7OzIXB8V0lRzgp/QJuLnU6Ua+jGXrxh9U=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,594 RestStorageService - Error Response: PUT '/GATK_Run_Reports/YZdfTTtcLqwbFZWMDuxsPp4MNeCkCvhh.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 814, x-amz-meta-md5-hash: 11e1fa5c716365dc62c3f94fb20acdc7, Content-Type: application/octet-stream, Content-MD5: EeH6XHFjZdxiw/lPsgrNxw==, Date: Thu, 22 Nov 2018 07:01:39 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:C8/U35TQhmIGCNJcViHM/nisq9w=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 8B1D7731D8207E18, x-amz-id-2: /wHRXek3OKxp48f0oSg1T4+sT8LnrwKNGX03ATPosjAL7z1VKL62Vwa+1LR1bsAZQiyMJ2osVuk=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,759 RestStorageService - Error Response: PUT '/GATK_Run_Reports/TCyEkthDoRUlWtNTby5RVxxJBnlOkllB.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 812, x-amz-meta-md5-hash: 83deffc1546e1ce1c47f08b19c1d6625, Content-Type: application/octet-stream, Content-MD5: g97/wVRuHOHEfwixnB1mJQ==, Date: Thu, 22 Nov 2018 07:01:39 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:18QRW7NJk5Aw+dKHuOYqisInd1c=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 65C41E369B0BEF3C, x-amz-id-2: 4mcaOjizm4X5Xy2c+oDLe4yEhSMfrjnWjg42rGo4hTtWBucfsKg+d45sZ1IL5/4/wN0G7+fOhv8=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
WARN  07:01:41,993 RestStorageService - Error Response: PUT '/GATK_Run_Reports/HaxgwTmtdmBIlUotyoHkCj8zIRYJi4Yt.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 813, x-amz-meta-md5-hash: 72aa2bfd9de4bb28b9898c8353b8ef1a, Content-Type: application/octet-stream, Content-MD5: cqor/Z3kuyi5iYyDU7jvGg==, Date: Thu, 22 Nov 2018 07:01:40 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:lA3pFlMUKZH88f8ayWzT0JIXvYQ=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-17134-Microsoft; amd64; en; JVM 1.8.0_191), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 44FEA86274ED883A, x-amz-id-2: 0X1PqJXKPnq4/arw/8lSEVU4C65clUNDTQSXhlzFwO5EA7HBHy5dwZSPd2A6TVRBdUvYbmLQXo0=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 22 Nov 2018 07:01:41 GMT, Connection: close, Server: AmazonS3]
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.germline.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.tumor.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.germline.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.tumor.recal

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not open dictionary file because a lock could not be obtained.
##### ERROR ------------------------------------------------------------------------------------------
ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.tumor.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.germline.recal


========================================= Pipeline Failed ==========================================

One or more parallel stages aborted. The following messages were reported:

--------------------------- gatk_depth_of_coverage  ( m14.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.tumor.recal

--------------------------- gatk_depth_of_coverage  ( m11.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.tumor.recal

------------------------- gatk_depth_of_coverage  ( m14.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.germline.recal

------------------------- gatk_depth_of_coverage  ( m11.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.germline.recal

------------------------- gatk_depth_of_coverage  ( m12.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.germline.recal

--------------------------- gatk_depth_of_coverage  ( m12.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/bin/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.tumor.recal

----------------------------------------------------------------------------------------------------

Use 'bpipe errors' to see output from failed commands.


Caught: java.lang.RuntimeException: Analysis failed for test/run1:
java.lang.RuntimeException: Analysis failed for test/run1:
        at Ximmer.runAnalysisForRun(Ximmer.groovy:462)
        at Ximmer$runAnalysisForRun$2.callCurrent(Unknown Source)
        at Ximmer.runAnalysis(Ximmer.groovy:337)
        at Ximmer$runAnalysis$1.callCurrent(Unknown Source)
        at Ximmer.run(Ximmer.groovy:199)
        at Ximmer$run.call(Unknown Source)
        at Ximmer.main(Ximmer.groovy:1279)

Can you please help me with this?

Does it happen with all callers ? Try to switch them one by one in config.qroovy (my ximmer installation unable to run Codex and Conifer, but other are ok).

Does Your reference file contain also index .fa.fai and fa.dict in the same folder ?

Yes it is giving errors with all others as well. Can you share your reference file? Yes i have .fai and .dict of my fasta

@SafinaAr
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Author

SafinaAr commented Jan 21, 2019 •
edited
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Can you please help me with this exception:

./bin/ximmer -v -nosim -c /mnt/d/AKU/FTP/BAM/config.groovy -o results
**************************************************

#     #  ###  #     #  #     #  #######  ######
 #   #    #   ##   ##  ##   ##  #        #     #
  # #     #   # # # #  # # # #  #        #     #
   #      #   #  #  #  #  #  #  #####    ######
  # #     #   #     #  #     #  #        #   #
 #   #    #   #     #  #     #  #        #    #
#     #  ###  #     #  #     #  #######  #     #

**************************************************
Configured verbose logging
Ximmer  [1]     INFO    |9:21:14 Configured verbose logging
Ximmer  [1]     INFO    |9:21:14 Simulation disabled.
Ximmer  [1]     INFO    |9:21:14 No run directory configured: run directory = run
Ximmer  [1]     INFO    |9:21:14 Configuration validated!
Ximmer  [1]     INFO    |9:21:14 Downloading DGV database from UCSC ...
Ximmer  [1]     INFO    |9:23:04 Downloading DGV database from UCSC ...
SimulationRun   [1]     INFO    |9:23:17 Resolved BAM files for run 1: [/mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam, /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam, /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam, /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam]
SimulationRun   [1]     INFO    |9:23:17 Processing BAM Files:
/mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam
/mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam
/mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam
/mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam
Ximmer  [1]     INFO    |9:23:17 Simulation disabled: analysis will be performed directly from source files
Ximmer  [1]     INFO    |9:23:17 No true positive CNVs configured for run 1
Ximmer  [1]     INFO    |9:23:17 Analysis has caller configuration: cnmops
Ximmer  [1]     INFO    |9:23:17 Anaysis keys are: []
Ximmer  [1]     INFO    |9:23:17 Write file results/run1/analysis/cnmops.default.params.txt with caller parameters
Ximmer  [1]     INFO    |9:23:17 Analysis has caller configuration: exomedepth
Ximmer  [1]     INFO    |9:23:17 Anaysis keys are: []
Ximmer  [1]     INFO    |9:23:17 Write file results/run1/analysis/ed.default.params.txt with caller parameters
Ximmer  [1]     INFO    |9:23:17 Analysis has caller configuration: conifer
Ximmer  [1]     INFO    |9:23:17 Anaysis keys are: []
Ximmer  [1]     INFO    |9:23:17 Write file results/run1/analysis/cfr.default.params.txt with caller parameters
Ximmer  [1]     INFO    |9:23:17 Executing Bpipe command: bash /home/sark/ximmer/eval/bpipe run -n 20 -p TOOLS=/home/sark/ximmer/eval/pipeline/tools -p DGV_CNVS=/home/sark/ximmer/cache/dgvMerged.txt.gz -p XIMMER_SRC=/home/sark/ximmer/src/main/groovy -p callers=cnmops,ed,cfr -p refgene=/home/sark/ximmer/cache/refGene.txt.gz -p simulation=false -p batches=analysis -p target_bed=/mnt/d/AKU/FTP/BAM/TruSeq_exome_targeted_regions.hg19.bed -p sample_id_mask="" -p imgpath=run1/#batch#/report/ /home/sark/ximmer/eval/pipeline/exome_cnv_pipeline.groovy /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam
====================================================================================================

  | |/ /(_)___ ___  ____ ___  ___  _____
  |   // / __ `__ \/ __ `__ \/ _ \/ ___/
 /   |/ / / / / / / / / / / /  __/ /
/_/|_/_/_/ /_/ /_/_/ /_/ /_/\___/_/

Ximmer Integrated CNV Analysis Pipeline

====================================================================================================
Scanning target region ...
Chromosomes for analysis are: [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX]
====================================================================================================
|                              Starting Pipeline at 2019-01-21 09:23                               |
====================================================================================================

============================================ Stage init ============================================

================================== Stage create_analysable_target ==================================

====================================== Stage init_common (1) =======================================
Running Common Stages

=========================== Stage gatk_depth_of_coverage (m11.germline) ============================

============================= Stage gatk_depth_of_coverage (m11.tumor) =============================

=========================== Stage gatk_depth_of_coverage (m12.germline) ============================

============================= Stage gatk_depth_of_coverage (m14.tumor) =============================

=========================== Stage gatk_depth_of_coverage (m14.germline) ============================

============================= Stage gatk_depth_of_coverage (m12.tumor) =============================
INFO  09:24:39,136 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  09:24:39,334 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,335 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  09:24:39,335 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  09:24:39,335 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  09:24:39,384 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m14.tumor.recal
INFO  09:24:39,413 HelpFormatter - Date/Time: 2019/01/21 09:24:39
INFO  09:24:39,413 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,413 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,136 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  09:24:39,327 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,327 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  09:24:39,327 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  09:24:39,328 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  09:24:39,384 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m12.germline.recal
INFO  09:24:39,413 HelpFormatter - Date/Time: 2019/01/21 09:24:39
INFO  09:24:39,413 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,413 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,136 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  09:24:39,319 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,320 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  09:24:39,320 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  09:24:39,320 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  09:24:39,384 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m12.tumor.recal
INFO  09:24:39,413 HelpFormatter - Date/Time: 2019/01/21 09:24:39
INFO  09:24:39,413 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,413 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:40,336 GenomeAnalysisEngine - Strictness is SILENT
INFO  09:24:40,470 ReferenceDataSource - Index file /mnt/d/AKU/FTP/human_gnme_refrnces.fai does not exist. Trying to create it now.
INFO  09:24:39,136 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  09:24:39,318 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,319 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  09:24:39,319 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  09:24:39,319 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  09:24:39,384 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m11.tumor.recal
INFO  09:24:39,412 HelpFormatter - Date/Time: 2019/01/21 09:24:39
INFO  09:24:39,412 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,413 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:40,336 GenomeAnalysisEngine - Strictness is SILENT
INFO  09:24:40,470 ReferenceDataSource - Index file /mnt/d/AKU/FTP/human_gnme_refrnces.fai does not exist. Trying to create it now.
INFO  09:24:39,136 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  09:24:39,321 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,322 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  09:24:39,322 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  09:24:39,322 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  09:24:39,384 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m14.germline.recal
INFO  09:24:39,412 HelpFormatter - Date/Time: 2019/01/21 09:24:39
INFO  09:24:39,412 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,413 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:40,336 GenomeAnalysisEngine - Strictness is SILENT
INFO  09:24:40,470 ReferenceDataSource - Index file /mnt/d/AKU/FTP/human_gnme_refrnces.fai does not exist. Trying to create it now.
INFO  09:24:39,136 ArgumentTypeDescriptor - Dynamically determined type of TruSeq_exome_targeted_regions.hg19.analysable.bed to be BED
INFO  09:24:39,321 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,322 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2018/05/06 13:31:46
INFO  09:24:39,322 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  09:24:39,322 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  09:24:39,384 HelpFormatter - Program Args: -T DepthOfCoverage -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o common/xhmm/m11.germline.recal
INFO  09:24:39,412 HelpFormatter - Date/Time: 2019/01/21 09:24:39
INFO  09:24:39,413 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:39,413 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:24:40,336 GenomeAnalysisEngine - Strictness is SILENT
INFO  09:24:40,470 ReferenceDataSource - Index file /mnt/d/AKU/FTP/human_gnme_refrnces.fai does not exist. Trying to create it now.
INFO  09:24:40,336 GenomeAnalysisEngine - Strictness is SILENT
INFO  09:24:40,470 ReferenceDataSource - Index file /mnt/d/AKU/FTP/human_gnme_refrnces.fai does not exist. Trying to create it now.
INFO  09:24:40,336 GenomeAnalysisEngine - Strictness is SILENT
INFO  09:24:40,470 ReferenceDataSource - Index file /mnt/d/AKU/FTP/human_gnme_refrnces.fai does not exist. Trying to create it now.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not read fasta file with exception /mnt/d/AKU/FTP/human_gnme_refrnces (Is a directory)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not read fasta file with exception /mnt/d/AKU/FTP/human_gnme_refrnces (Is a directory)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not read fasta file with exception /mnt/d/AKU/FTP/human_gnme_refrnces (Is a directory)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not read fasta file with exception /mnt/d/AKU/FTP/human_gnme_refrnces (Is a directory)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not read fasta file with exception /mnt/d/AKU/FTP/human_gnme_refrnces (Is a directory)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Couldn't read file /mnt/d/AKU/FTP/human_gnme_refrnces because Could not read fasta file with exception /mnt/d/AKU/FTP/human_gnme_refrnces (Is a directory)
##### ERROR ------------------------------------------------------------------------------------------
ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.tumor.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.germline.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.germline.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.tumor.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.tumor.recal

ERROR: stage gatk_depth_of_coverage failed: Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.germline.recal


========================================= Pipeline Failed ==========================================

One or more parallel stages aborted. The following messages were reported:

--------------------------- gatk_depth_of_coverage  ( m12.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.tumor.recal

------------------------- gatk_depth_of_coverage  ( m11.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.germline.recal

--------------------------- gatk_depth_of_coverage  ( m11.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m11.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m11.tumor.recal

------------------------- gatk_depth_of_coverage  ( m14.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.germline.recal

--------------------------- gatk_depth_of_coverage  ( m14.tumor.recal )  ---------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m14.tumor.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m14.tumor.recal

------------------------- gatk_depth_of_coverage  ( m12.germline.recal )  --------------------------

Command in stage gatk_depth_of_coverage failed with exit status = 1 :

java -Xmx2g -Djava.io.tmpdir=tmpdata -jar /home/sark/ximmer/eval/pipeline/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T DepthOfCoverage  -I /mnt/d/AKU/FTP/BAMonly/m12.germline.recal.bam -L TruSeq_exome_targeted_regions.hg19.analysable.bed -R /mnt/d/AKU/FTP/human_gnme_refrnces/ -dt BY_SAMPLE  -dcov 5000  -l INFO  --omitDepthOutputAtEachBase  --omitLocusTable  --minBaseQuality 0  --minMappingQuality 20  --start 1  --stop 5000  --nBins 200  --includeRefNSites  --countType COUNT_FRAGMENTS  -o common/xhmm/m12.germline.recal

----------------------------------------------------------------------------------------------------

Use 'bpipe errors' to see output from failed commands.


Caught: java.lang.RuntimeException: Analysis failed for results/run1:
java.lang.RuntimeException: Analysis failed for results/run1:
        at Ximmer.runAnalysisForRun(Ximmer.groovy:462)
        at Ximmer$runAnalysisForRun$2.callCurrent(Unknown Source)
        at Ximmer.runAnalysis(Ximmer.groovy:337)
        at Ximmer$runAnalysis$1.callCurrent(Unknown Source)
        at Ximmer.run(Ximmer.groovy:199)
        at Ximmer$run.call(Unknown Source)
        at Ximmer.main(Ximmer.groovy:1279)

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@ssadedin @SafinaAr @bopohdr