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test qualimap_bamqc 2.2.2d+galaxy3 + 2.2.2c #70

Closed
jennaj opened this issue Nov 18, 2022 · 4 comments
Closed

test qualimap_bamqc 2.2.2d+galaxy3 + 2.2.2c #70

jennaj opened this issue Nov 18, 2022 · 4 comments

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@jennaj
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jennaj commented Nov 18, 2022

toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c
@jennaj
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Collaborator Author

jennaj commented Nov 18, 2022

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3

@mvdbeek
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mvdbeek commented Nov 18, 2022

Results (powered by Planemo)

Summary

State Count
Total 5
Passed 5
Error 0
Failure 0
Skipped 0
Passed s
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc (Test tool test #1)

    Command Line:

    • 

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/897/46897493/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/897/46897493/_job_tmp -Xmx28g -Xms256m

      

      • 

    

    Standard Output:
    

      

    • 

      Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx30720m
QualiMap v.2.2.2-dev
Built on 2019-11-11 14:05

Selected tool: bamqc
Available memory (Mb): 268
Max memory (Mb): 30064
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 325
Chunk of reads size: 1000
Number of threads: 6
Processed 50 out of 325 windows...
Processed 100 out of 325 windows...
Processed 150 out of 325 windows...
Processed 200 out of 325 windows...
Processed 250 out of 325 windows...
Processed 300 out of 325 windows...
Total processed windows:325
Number of reads: 100
Number of valid reads: 100
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 100
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 0
Computing descriptors...
numberOfMappedBases: 12665
referenceSize: 650
numberOfSequencedBases: 7465
numberOfAs: 1910
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 0
end of bam qc
Computing report...
Writing HTML report...
HTML report created successfully

Finished

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
dbkey
"?"

      

      
__input_ext
"bam"

      

      
stats_regions
{"__current_case__": 0, "region_select": "all"}

      

      
per_base_coverage
"false"

      

      
duplicate_skipping
"0"

      

      
plot_specific
{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": "true"}

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc (Test test against test.galaxyproject.org #2)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/897/46897508/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/897/46897508/_job_tmp -Xmx28g -Xms256m

      

      • 

    

    Standard Output:
    

      

    • 

      Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx30720m
QualiMap v.2.2.2-dev
Built on 2019-11-11 14:05

Selected tool: bamqc
Available memory (Mb): 268
Max memory (Mb): 30064
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 325
Chunk of reads size: 1000
Number of threads: 6
Processed 50 out of 325 windows...
Processed 100 out of 325 windows...
Processed 150 out of 325 windows...
Processed 200 out of 325 windows...
Processed 250 out of 325 windows...
Processed 300 out of 325 windows...
Total processed windows:325
Number of reads: 100
Number of valid reads: 100
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 100
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 0
Computing descriptors...
numberOfMappedBases: 12665
referenceSize: 650
numberOfSequencedBases: 7465
numberOfAs: 1910
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 0
end of bam qc
Computing report...
Writing HTML report...
HTML report created successfully

Finished

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
stats_regions
{"__current_case__": 0, "region_select": "all"}

      

      
per_base_coverage
"true"

      

      
duplicate_skipping
"0"

      

      
plot_specific
{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": "true"}

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"bam"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/897/46897580/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/897/46897580/_job_tmp -Xmx28g -Xms256m

      

      • 

    

    Standard Output:
    

      

    • 

      Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx30720m
QualiMap v.2.2.2-dev
Built on 2019-11-11 14:05

Selected tool: bamqc
Available memory (Mb): 268
Max memory (Mb): 30064
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 325
Chunk of reads size: 1000
Number of threads: 6
Initializing regions from regions.gtf.....
Found 4 regions
Filling region references... 
Processed 50 out of 325 windows...
Processed 100 out of 325 windows...
Processed 150 out of 325 windows...
Processed 200 out of 325 windows...
Processed 250 out of 325 windows...
Processed 300 out of 325 windows...
Total processed windows:325
Number of reads: 100
Number of valid reads: 100
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 82
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 0
Computing descriptors...
numberOfMappedBases: 6451
referenceSize: 650
numberOfSequencedBases: 5101
numberOfAs: 1243
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 0
end of bam qc
Computing report...
Writing HTML report...
HTML report created successfully

Finished

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
stats_regions
{"__current_case__": 1, "outside_stats": "false", "region_select": "custom_regions", "regions": {"values": [{"id": 105221977, "src": "hda"}]}}

      

      
per_base_coverage
"false"

      

      
duplicate_skipping
"0"

      

      
plot_specific
{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": "true"}

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"bam"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc (Test Test roary 3.13.0+galaxy2 #4)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/897/46897520/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/897/46897520/_job_tmp -Xmx28g -Xms256m

      

      • 

    

    Standard Output:
    

      

    • 

      Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx30720m
QualiMap v.2.2.2-dev
Built on 2019-11-11 14:05

Selected tool: bamqc
Available memory (Mb): 268
Max memory (Mb): 30064
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 325
Chunk of reads size: 1000
Number of threads: 6
Initializing regions from regions.gtf.....
Found 4 regions
Filling region references... 
Processed 50 out of 325 windows...
Processed 100 out of 325 windows...
Processed 150 out of 325 windows...
Processed 200 out of 325 windows...
Processed 250 out of 325 windows...
Processed 300 out of 325 windows...
Total processed windows:325
Number of reads: 100
Number of valid reads: 100
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 82
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 8
Computing descriptors...
numberOfMappedBases: 6451
referenceSize: 650
numberOfSequencedBases: 5101
numberOfAs: 1243
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 10
end of bam qc
Computing report...
Writing HTML report...
HTML report created successfully

Finished

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
stats_regions
{"__current_case__": 1, "outside_stats": "false", "region_select": "custom_regions", "regions": {"values": [{"id": 105221977, "src": "hda"}]}}

      

      
per_base_coverage
"true"

      

      
duplicate_skipping
"0"

      

      
plot_specific
{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": "true"}

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"bam"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/897/46897494/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/897/46897494/_job_tmp -Xmx28g -Xms256m

      

      • 

    

    Standard Output:
    

      

    • 

      Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx30720m
QualiMap v.2.2.2-dev
Built on 2019-11-11 14:05

Selected tool: bamqc
Available memory (Mb): 268
Max memory (Mb): 30064
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 325
Chunk of reads size: 1000
Number of threads: 6
Initializing regions from regions.gtf.....
Found 4 regions
Filling region references... 
Processed 50 out of 325 windows...
Processed 100 out of 325 windows...
Processed 150 out of 325 windows...
Processed 200 out of 325 windows...
Processed 250 out of 325 windows...
Processed 300 out of 325 windows...
Total processed windows:325
Number of reads: 100
Number of valid reads: 100
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 82
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0

Ouside of regions...
Num mapped reads: 18
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 0
Computing descriptors...
numberOfMappedBases: 6451
referenceSize: 650
numberOfSequencedBases: 5101
numberOfAs: 1243
Computing per chromosome statistics...
Computing histograms...
Computing descriptors for outside regions...
numberOfMappedBases: 6214
referenceSize: 650
numberOfSequencedBases: 2364
numberOfAs: 667
Computing per chromosome statistics for outside regions...
Computing histograms for outside regions...
Overall analysis time: 0
end of bam qc
Computing report...
Writing HTML report...
HTML report created successfully

Finished

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
stats_regions
{"__current_case__": 1, "outside_stats": "true", "region_select": "custom_regions", "regions": {"values": [{"id": 105221977, "src": "hda"}]}}

      

      
per_base_coverage
"true"

      

      
duplicate_skipping
"0"

      

      
plot_specific
{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": "true"}

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"bam"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
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  Author


  


  

    

      

      
            jennaj
  

      

      

      commented


        Nov 18, 2022


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Owner


      

  


  

    

      

      
            mvdbeek
  

      

      

      commented


        Nov 18, 2022


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
5




Passed
0




Error
0




Failure
5




Skipped
0






Failed s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc (Test tool test #1)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898642/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898642/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898642/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898642/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Collection element genome_results of collection raw_data:  different than expected, difference (using diff):
( /tmp/tmpe9i8kw6vgenome_results_default.txt v. /tmp/tmp841bj316genome_results_default.txt )
--- local_file
+++ history_data
@@ -1,122 +0,0 @@
-BamQC report
------------------------------------
-
->>>>>>> Input
-
-     bam file = /tmp/tmprT4oZK/files/b/1/f/dataset_b1fbaad4-1b5a-4769-8a15-b4cec4de5731.dat
-     outfile = results/genome_results.txt
-
-
->>>>>>> Reference
-
-     number of bases = 650 bp
-     number of contigs = 1
-
-
->>>>>>> Globals
-
-     number of windows = 325
-
-     number of reads = 100
-     number of mapped reads = 100 (100%)
-     number of secondary alignments = 1
********
*SNIP *
********
-     There is a 10.15% of reference with a coverageData >= 34X
-     There is a 8.62% of reference with a coverageData >= 35X
-     There is a 7.38% of reference with a coverageData >= 36X
-     There is a 4% of reference with a coverageData >= 37X
-     There is a 1.85% of reference with a coverageData >= 38X
-     There is a 0.31% of reference with a coverageData >= 39X
-     There is a 0% of reference with a coverageData >= 40X
-     There is a 0% of reference with a coverageData >= 41X
-     There is a 0% of reference with a coverageData >= 42X
-     There is a 0% of reference with a coverageData >= 43X
-     There is a 0% of reference with a coverageData >= 44X
-     There is a 0% of reference with a coverageData >= 45X
-     There is a 0% of reference with a coverageData >= 46X
-     There is a 0% of reference with a coverageData >= 47X
-     There is a 0% of reference with a coverageData >= 48X
-     There is a 0% of reference with a coverageData >= 49X
-     There is a 0% of reference with a coverageData >= 50X
-     There is a 0% of reference with a coverageData >= 51X
-
-
->>>>>>> Coverage per contig
-
-	test_chromosome	650	12665	19.484615384615385	16.581284452141826
-
-


      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898642/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898642/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more

      

      • 

    

    Standard Output:
    

      

    • 

      Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx30720m
QualiMap v.2.2.2-dev
Built on 2018-12-03 16:04

Selected tool: bamqc
Available memory (Mb): 268
Max memory (Mb): 30064
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 325
Chunk of reads size: 1000
Number of threads: 6
Processed 50 out of 325 windows...
Processed 100 out of 325 windows...
Processed 150 out of 325 windows...
Processed 200 out of 325 windows...
Processed 250 out of 325 windows...
Processed 300 out of 325 windows...
Total processed windows:325
Number of reads: 100
Number of valid reads: 100
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 100
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 0
Computing descriptors...
numberOfMappedBases: 12665
referenceSize: 650
numberOfSequencedBases: 7465
numberOfAs: 1910
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 0
end of bam qc
Computing report...
Writing HTML report...

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
stats_regions
{"__current_case__": 0, "region_select": "all"}

      

      
per_base_coverage
"false"

      

      
duplicate_skipping
"0"

      

      
plot_specific
{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": "true"}

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"bam"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898618/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898618/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898618/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898618/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898618/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898618/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Collection element genome_results of collection raw_data:  different than expected, difference (using diff):
( /tmp/tmpnmh39uvygenome_results_default.txt v. /tmp/tmpp0hsyzzxgenome_results_default.txt )
--- local_file
+++ history_data
@@ -1,122 +0,0 @@
-BamQC report
------------------------------------
-
->>>>>>> Input
-
-     bam file = /tmp/tmprT4oZK/files/b/1/f/dataset_b1fbaad4-1b5a-4769-8a15-b4cec4de5731.dat
-     outfile = results/genome_results.txt
-
-
->>>>>>> Reference
-
-     number of bases = 650 bp
-     number of contigs = 1
-
-
->>>>>>> Globals
-
-     number of windows = 325
-
-     number of reads = 100
-     number of mapped reads = 100 (100%)
-     number of secondary alignments = 1
********
*SNIP *
********
-     There is a 10.15% of reference with a coverageData >= 34X
-     There is a 8.62% of reference with a coverageData >= 35X
-     There is a 7.38% of reference with a coverageData >= 36X
-     There is a 4% of reference with a coverageData >= 37X
-     There is a 1.85% of reference with a coverageData >= 38X
-     There is a 0.31% of reference with a coverageData >= 39X
-     There is a 0% of reference with a coverageData >= 40X
-     There is a 0% of reference with a coverageData >= 41X
-     There is a 0% of reference with a coverageData >= 42X
-     There is a 0% of reference with a coverageData >= 43X
-     There is a 0% of reference with a coverageData >= 44X
-     There is a 0% of reference with a coverageData >= 45X
-     There is a 0% of reference with a coverageData >= 46X
-     There is a 0% of reference with a coverageData >= 47X
-     There is a 0% of reference with a coverageData >= 48X
-     There is a 0% of reference with a coverageData >= 49X
-     There is a 0% of reference with a coverageData >= 50X
-     There is a 0% of reference with a coverageData >= 51X
-
-
->>>>>>> Coverage per contig
-
-	test_chromosome	650	12665	19.484615384615385	16.581284452141826
-
-


      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898618/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898618/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more

      

      • 

    

    Standard Output:
    

      

    • 

      Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx30720m
QualiMap v.2.2.2-dev
Built on 2018-12-03 16:04

Selected tool: bamqc
Available memory (Mb): 268
Max memory (Mb): 30064
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 325
Chunk of reads size: 1000
Number of threads: 6
Processed 50 out of 325 windows...
Processed 100 out of 325 windows...
Processed 150 out of 325 windows...
Processed 200 out of 325 windows...
Processed 250 out of 325 windows...
Processed 300 out of 325 windows...
Total processed windows:325
Number of reads: 100
Number of valid reads: 100
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 100
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 0
Computing descriptors...
numberOfMappedBases: 12665
referenceSize: 650
numberOfSequencedBases: 7465
numberOfAs: 1910
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 0
end of bam qc
Computing report...
Writing HTML report...

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
stats_regions
{"__current_case__": 0, "region_select": "all"}

      

      
per_base_coverage
"true"

      

      
duplicate_skipping
"0"

      

      
plot_specific
{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": "true"}

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"auto"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898626/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898626/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898626/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898626/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Collection element genome_results of collection raw_data:  different than expected, difference (using diff):
( /tmp/tmpdbbkqgz7genome_results_inside_features.txt v. /tmp/tmp0x0rst5sgenome_results_inside_features.txt )
--- local_file
+++ history_data
@@ -1,128 +0,0 @@
-BamQC report
------------------------------------
-
->>>>>>> Input
-
-     bam file = /tmp/tmpB4Sf0A/files/e/d/7/dataset_ed7510d4-c8f3-41fc-8cc1-3b854d9bdf14.dat
-     outfile = results/genome_results.txt
-
-
->>>>>>> Reference
-
-     number of bases = 650 bp
-     number of contigs = 1
-
-
->>>>>>> Globals
-
-     number of windows = 325
-
-     number of reads = 100
-     number of mapped reads = 100 (100%)
-     number of secondary alignments = 1
********
*SNIP *
********
-     There is a 13% of reference with a coverageData >= 34X
-     There is a 11.33% of reference with a coverageData >= 35X
-     There is a 10% of reference with a coverageData >= 36X
-     There is a 5.67% of reference with a coverageData >= 37X
-     There is a 3% of reference with a coverageData >= 38X
-     There is a 0% of reference with a coverageData >= 39X
-     There is a 0% of reference with a coverageData >= 40X
-     There is a 0% of reference with a coverageData >= 41X
-     There is a 0% of reference with a coverageData >= 42X
-     There is a 0% of reference with a coverageData >= 43X
-     There is a 0% of reference with a coverageData >= 44X
-     There is a 0% of reference with a coverageData >= 45X
-     There is a 0% of reference with a coverageData >= 46X
-     There is a 0% of reference with a coverageData >= 47X
-     There is a 0% of reference with a coverageData >= 48X
-     There is a 0% of reference with a coverageData >= 49X
-     There is a 0% of reference with a coverageData >= 50X
-     There is a 0% of reference with a coverageData >= 51X
-
-
->>>>>>> Coverage per contig
-
-	test_chromosome	300	6451	21.503333333333334	15.658011438947867
-
-


      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898626/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898626/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more

      

      • 

    

    Standard Output:
    

      

    • 

      Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx30720m
QualiMap v.2.2.2-dev
Built on 2018-12-03 16:04

Selected tool: bamqc
Available memory (Mb): 268
Max memory (Mb): 30064
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 325
Chunk of reads size: 1000
Number of threads: 6
Initializing regions from /corral4/main/objects/8/9/4/dataset_8943627b-1ced-4da5-861d-936eae38e363.dat.....
Found 4 regions
Filling region references... 
Processed 50 out of 325 windows...
Processed 100 out of 325 windows...
Processed 150 out of 325 windows...
Processed 200 out of 325 windows...
Processed 250 out of 325 windows...
Processed 300 out of 325 windows...
Total processed windows:325
Number of reads: 100
Number of valid reads: 100
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 82
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 0
Computing descriptors...
numberOfMappedBases: 6451
referenceSize: 650
numberOfSequencedBases: 5101
numberOfAs: 1243
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 0
end of bam qc
Computing report...
Writing HTML report...

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
stats_regions
{"__current_case__": 1, "outside_stats": "false", "region_select": "custom_regions", "regions": {"values": [{"id": 105224160, "src": "hda"}]}}

      

      
per_base_coverage
"false"

      

      
duplicate_skipping
"0"

      

      
plot_specific
{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": "true"}

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"bam"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc (Test Test roary 3.13.0+galaxy2 #4)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898634/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898634/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898634/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898634/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898634/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898634/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Collection element genome_results of collection raw_data:  different than expected, difference (using diff):
( /tmp/tmphf1k5z52genome_results_inside_features.txt v. /tmp/tmpkx1q9iskgenome_results_inside_features.txt )
--- local_file
+++ history_data
@@ -1,128 +0,0 @@
-BamQC report
------------------------------------
-
->>>>>>> Input
-
-     bam file = /tmp/tmpB4Sf0A/files/e/d/7/dataset_ed7510d4-c8f3-41fc-8cc1-3b854d9bdf14.dat
-     outfile = results/genome_results.txt
-
-
->>>>>>> Reference
-
-     number of bases = 650 bp
-     number of contigs = 1
-
-
->>>>>>> Globals
-
-     number of windows = 325
-
-     number of reads = 100
-     number of mapped reads = 100 (100%)
-     number of secondary alignments = 1
********
*SNIP *
********
-     There is a 13% of reference with a coverageData >= 34X
-     There is a 11.33% of reference with a coverageData >= 35X
-     There is a 10% of reference with a coverageData >= 36X
-     There is a 5.67% of reference with a coverageData >= 37X
-     There is a 3% of reference with a coverageData >= 38X
-     There is a 0% of reference with a coverageData >= 39X
-     There is a 0% of reference with a coverageData >= 40X
-     There is a 0% of reference with a coverageData >= 41X
-     There is a 0% of reference with a coverageData >= 42X
-     There is a 0% of reference with a coverageData >= 43X
-     There is a 0% of reference with a coverageData >= 44X
-     There is a 0% of reference with a coverageData >= 45X
-     There is a 0% of reference with a coverageData >= 46X
-     There is a 0% of reference with a coverageData >= 47X
-     There is a 0% of reference with a coverageData >= 48X
-     There is a 0% of reference with a coverageData >= 49X
-     There is a 0% of reference with a coverageData >= 50X
-     There is a 0% of reference with a coverageData >= 51X
-
-
->>>>>>> Coverage per contig
-
-	test_chromosome	300	6451	21.503333333333334	15.658011438947867
-
-


      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898634/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898634/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more

      

      • 

    

    Standard Output:
    

      

    • 

      Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx30720m
QualiMap v.2.2.2-dev
Built on 2018-12-03 16:04

Selected tool: bamqc
Available memory (Mb): 268
Max memory (Mb): 30064
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 325
Chunk of reads size: 1000
Number of threads: 6
Initializing regions from /corral4/main/objects/8/9/4/dataset_8943627b-1ced-4da5-861d-936eae38e363.dat.....
Found 4 regions
Filling region references... 
Processed 50 out of 325 windows...
Processed 100 out of 325 windows...
Processed 150 out of 325 windows...
Processed 200 out of 325 windows...
Processed 250 out of 325 windows...
Processed 300 out of 325 windows...
Total processed windows:325
Number of reads: 100
Number of valid reads: 100
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 82
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 0
Computing descriptors...
numberOfMappedBases: 6451
referenceSize: 650
numberOfSequencedBases: 5101
numberOfAs: 1243
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 0
end of bam qc
Computing report...
Writing HTML report...

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
stats_regions
{"__current_case__": 1, "outside_stats": "false", "region_select": "custom_regions", "regions": {"values": [{"id": 105224160, "src": "hda"}]}}

      

      
per_base_coverage
"true"

      

      
duplicate_skipping
"0"

      

      
plot_specific
{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": "true"}

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"bam"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898625/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898625/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898625/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898625/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c, exit_code: 1, stderr: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898625/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898625/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more
.

      

      • 

    • 

      Collection element genome_results of collection raw_data:  different than expected, difference (using diff):
( /tmp/tmp4mz44jkagenome_results_outside_features.txt v. /tmp/tmpofxv9qbzgenome_results_outside_features.txt )
--- local_file
+++ history_data
@@ -1,128 +0,0 @@
-BamQC report
------------------------------------
-
->>>>>>> Input
-
-     bam file = /tmp/tmprT4oZK/files/6/4/1/dataset_6416c0ca-3ecd-4273-ae01-22f2ac60965d.dat
-     outfile = results/outside_results.txt
-
-
->>>>>>> Reference
-
-     number of bases = 650 bp
-     number of contigs = 1
-
-
->>>>>>> Globals
-
-     number of windows = 325
-
-     number of reads = 100
-     number of mapped reads = 100 (100%)
-     number of secondary alignments = 1
********
*SNIP *
********
-     There is a 9.13% of reference with a coverageData >= 34X
-     There is a 7.21% of reference with a coverageData >= 35X
-     There is a 5.29% of reference with a coverageData >= 36X
-     There is a 3.37% of reference with a coverageData >= 37X
-     There is a 1.44% of reference with a coverageData >= 38X
-     There is a 0.96% of reference with a coverageData >= 39X
-     There is a 0% of reference with a coverageData >= 40X
-     There is a 0% of reference with a coverageData >= 41X
-     There is a 0% of reference with a coverageData >= 42X
-     There is a 0% of reference with a coverageData >= 43X
-     There is a 0% of reference with a coverageData >= 44X
-     There is a 0% of reference with a coverageData >= 45X
-     There is a 0% of reference with a coverageData >= 46X
-     There is a 0% of reference with a coverageData >= 47X
-     There is a 0% of reference with a coverageData >= 48X
-     There is a 0% of reference with a coverageData >= 49X
-     There is a 0% of reference with a coverageData >= 50X
-     There is a 0% of reference with a coverageData >= 51X
-
-
->>>>>>> Coverage per contig
-
-	test_chromosome	4424	6214	1.404611211573237	3.9981701358234454
-
-


      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      1
      

      • 

    

    Standard Error:
    

      

    • 

      Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898625/_job_tmp -Xmx28g -Xms256m
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/046/898/46898625/_job_tmp -Xmx28g -Xms256m
Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
	at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
	at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
	at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
	at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
	at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
	at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
	at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
	at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
	at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
	at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
	at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
	at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
	at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
	at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
	... 22 more
Caused by: java.lang.NullPointerException
	at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
	at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
	at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
	at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
	at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
	at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
	at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
	... 27 more

      

      • 

    

    Standard Output:
    

      

    • 

      Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx30720m
QualiMap v.2.2.2-dev
Built on 2018-12-03 16:04

Selected tool: bamqc
Available memory (Mb): 268
Max memory (Mb): 30064
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Only flagged duplicate alignments will be skipped...
Number of windows: 400, effective number of windows: 325
Chunk of reads size: 1000
Number of threads: 6
Initializing regions from /corral4/main/objects/8/9/4/dataset_8943627b-1ced-4da5-861d-936eae38e363.dat.....
Found 4 regions
Filling region references... 
Processed 50 out of 325 windows...
Processed 100 out of 325 windows...
Processed 150 out of 325 windows...
Processed 200 out of 325 windows...
Processed 250 out of 325 windows...
Processed 300 out of 325 windows...
Total processed windows:325
Number of reads: 100
Number of valid reads: 100
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 82
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0

Ouside of regions...
Num mapped reads: 18
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 0
Computing descriptors...
numberOfMappedBases: 6451
referenceSize: 650
numberOfSequencedBases: 5101
numberOfAs: 1243
Computing per chromosome statistics...
Computing histograms...
Computing descriptors for outside regions...
numberOfMappedBases: 6214
referenceSize: 650
numberOfSequencedBases: 2364
numberOfAs: 667
Computing per chromosome statistics for outside regions...
Computing histograms for outside regions...
Overall analysis time: 0
end of bam qc
Computing report...
Writing HTML report...

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
stats_regions
{"__current_case__": 1, "outside_stats": "true", "region_select": "custom_regions", "regions": {"values": [{"id": 105224160, "src": "hda"}]}}

      

      
per_base_coverage
"true"

      

      
duplicate_skipping
"0"

      

      
plot_specific
{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": "true"}

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"auto"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    

      
    

    


      

          @jennaj
jennaj




            closed this as completed


      Jan 11, 2023

    

  


    











  
  

    

      

  





  




  
  

              

  
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          @mvdbeek 
        
          @jennaj