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Old 05-20-2011, 03:05 AM   #1
yimaizhe
LQ Newbie
 
Registered: May 2011
Posts: 11

Rep: Reputation: Disabled
Red face Help to solve a java problem maybe


Hi,

I installed birdsuite <http://www.broadinstitute.org/scient...uite/birdsuite >
(A genetics software used to detect SNP and CNV) on ubuntu10.10 platform

After installing the software following the instructions list on the web,
I run it ,whereas it comes out to be errors :

1> java.lang.reflect.InvocationTargetException

2> java.io.IOException

Could you please help me to solve it or tell me why?
Much obliged.
The reboust command line and results are as follows:

bhli@ubuntu:~/TESTDIR$ ~/EXEDIR/birdsuite.sh --basename=test --exeDir=/home/bhli/EXEDIR/ --metadataDir=/home/bhli/METADATADIR/ --chipType=GenomeWideSNP_6 --genderFile=/home/bhli/TESTDIR/test.gender --celFiles=/home/bhli/TESTDIR/test.cels --noLsf --apt_probeset_summarize.force --outputDir=output
+ unset DISPLAY
+ export MCR_INHIBIT_CTF_LOCK=1
+ MCR_INHIBIT_CTF_LOCK=1
++ /home/bhli/EXEDIR/getAbsPath /home/bhli/EXEDIR
+ exedir=/home/bhli/EXEDIR
+ export R_LIBS=/home/bhli/EXEDIR:
+ R_LIBS=/home/bhli/EXEDIR:
+ '[' -n 1 ']'
+ exedir_args=--exeDir=/home/bhli/EXEDIR
+ java -jar /home/bhli/EXEDIR/Birdsuite.jar --exeDir=/home/bhli/EXEDIR --basename=test --exeDir=/home/bhli/EXEDIR/ --metadataDir=/home/bhli/METADATADIR/ --chipType=GenomeWideSNP_6 --genderFile=/home/bhli/TESTDIR/test.gender --celFiles=/home/bhli/TESTDIR/test.cels --noLsf --apt_probeset_summarize.force --outputDir=output
Newer version of birdsuite available. Version running is 1.5.5 latest version is 1.5.2
Fri May 20 14:13:03 CST 2011 Calling /home/bhli/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /home/bhli/METADATADIR/GenomeWideSNP_6.Full.cdf --probeset-ids /home/bhli/METADATADIR/GenomeWideSNP_6.birdsuite_probelist --mem-usage 4000 --block-size 0 --precision 2 --force cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A01_31218.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A02_31234.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A03_31250.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A04_31266.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A05_31282.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A06_31298.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A07_31314.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A08_31330.CEL
Opening cdf file: GenomeWideSNP_6.Full.cdf
Expecting 1 iteration.
Doing iteration: 1
Opening cdf file: GenomeWideSNP_6.Full.cdf
Loading 1842537 probesets and 6675129 probes.
Reading 8 cel filesDone.
Processing Probesets......................Done.
Flushing output reporters. Finalizing output.
Done.
Cleaning up.
Done.
Run took approximately: 3.33 minutes.
Fri May 20 14:16:24 CST 2011 Done /home/bhli/EXEDIR/apt-probeset-summarize.sh
Fri May 20 14:16:24 CST 2011 Calling /home/bhli/EXEDIR/cn_annotate_allele_summary --probe_locus /home/bhli/METADATADIR/GenomeWideSNP_6.hg18.probe_locus -o output/test.annotated_summary -t output --summary output/test.allele_summary

Exception in thread "main" edu.mit.broad.mpgcore.exception.MPGRuntimeException: java.lang.reflect.InvocationTargetException
at edu.mit.broad.espcore.apps.affy.BirdSuite.run(BirdSuite.java:401)
at edu.mit.broad.espcore.apps.affy.BirdSuite.main(BirdSuite.java:296)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at edu.mit.broad.espcore.apps.affy.BirdSuite.run(BirdSuite.java:396)
... 1 more
Caused by: edu.mit.broad.mpgcore.exception.MPGRuntimeException: java.io.IOException: Cannot run program "/home/bhli/EXEDIR/cn_annotate_allele_summary": java.io.IOException: error=2, No such file or directory
at edu.mit.broad.espcore.apps.affy.BirdSuite.execWithStdOutputs(BirdSuite.java:359)
at edu.mit.broad.espcore.apps.affy.BirdSuite.annotate_allele_summaries(BirdSuite.java:478)
... 6 more
Caused by: java.io.IOException: Cannot run program "/home/bhli/EXEDIR/cn_annotate_allele_summary": java.io.IOException: error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at java.lang.Runtime.exec(Runtime.java:593)
at edu.mit.broad.espcore.apps.affy.BirdSuite.execWithStdOutputs(BirdSuite.java:335)
... 7 more
Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
at java.lang.ProcessImpl.start(ProcessImpl.java:65)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
... 9 more
 
Old 05-20-2011, 09:12 PM   #2
Hevithan
Member
 
Registered: Apr 2011
Location: Washington State
Distribution: Zorin5-(Ubuntu 11.04) // Backtrack 5-(Ubuntu 10.04) // Dreamlinux 3.5-(Debian)
Posts: 275
Blog Entries: 5

Rep: Reputation: 40
Sorry I don't know how to help with your JAVA problem, But when you post code, if you do this:

{code} INSERT CODE HERE {/code} ... Replacing { and } with [ and ]

It makes it easier for people to read and doesn't take a ton of room. Like so:

Code:
bhli@ubuntu:~/TESTDIR$ ~/EXEDIR/birdsuite.sh --basename=test --exeDir=/home/bhli/EXEDIR/ --metadataDir=/home/bhli/METADATADIR/ --chipType=GenomeWideSNP_6 --genderFile=/home/bhli/TESTDIR/test.gender --celFiles=/home/bhli/TESTDIR/test.cels --noLsf --apt_probeset_summarize.force --outputDir=output
+ unset DISPLAY
+ export MCR_INHIBIT_CTF_LOCK=1
+ MCR_INHIBIT_CTF_LOCK=1
++ /home/bhli/EXEDIR/getAbsPath /home/bhli/EXEDIR
+ exedir=/home/bhli/EXEDIR
+ export R_LIBS=/home/bhli/EXEDIR:
+ R_LIBS=/home/bhli/EXEDIR:
+ '[' -n 1 ']'
+ exedir_args=--exeDir=/home/bhli/EXEDIR
+ java -jar /home/bhli/EXEDIR/Birdsuite.jar --exeDir=/home/bhli/EXEDIR --basename=test --exeDir=/home/bhli/EXEDIR/ --metadataDir=/home/bhli/METADATADIR/ --chipType=GenomeWideSNP_6 --genderFile=/home/bhli/TESTDIR/test.gender --celFiles=/home/bhli/TESTDIR/test.cels --noLsf --apt_probeset_summarize.force --outputDir=output
Newer version of birdsuite available. Version running is 1.5.5 latest version is 1.5.2
Fri May 20 14:13:03 CST 2011 Calling /home/bhli/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /home/bhli/METADATADIR/GenomeWideSNP_6.Full.cdf --probeset-ids /home/bhli/METADATADIR/GenomeWideSNP_6.birdsuite_probelist --mem-usage 4000 --block-size 0 --precision 2 --force cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A01_31218.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A02_31234.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A03_31250.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A04_31266.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A05_31282.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A06_31298.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A07_31314.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A08_31330.CEL
Opening cdf file: GenomeWideSNP_6.Full.cdf
Expecting 1 iteration.
Doing iteration: 1
Opening cdf file: GenomeWideSNP_6.Full.cdf
Loading 1842537 probesets and 6675129 probes.
Reading 8 cel filesDone.
Processing Probesets......................Done.
Flushing output reporters. Finalizing output.
Done.
Cleaning up.
Done.
Run took approximately: 3.33 minutes.
Fri May 20 14:16:24 CST 2011 Done /home/bhli/EXEDIR/apt-probeset-summarize.sh
Fri May 20 14:16:24 CST 2011 Calling /home/bhli/EXEDIR/cn_annotate_allele_summary --probe_locus /home/bhli/METADATADIR/GenomeWideSNP_6.hg18.probe_locus -o output/test.annotated_summary -t output --summary output/test.allele_summary

Exception in thread "main" edu.mit.broad.mpgcore.exception.MPGRuntimeException: java.lang.reflect.InvocationTargetException
at edu.mit.broad.espcore.apps.affy.BirdSuite.run(BirdSuite.java:401)
at edu.mit.broad.espcore.apps.affy.BirdSuite.main(BirdSuite.java:296)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at edu.mit.broad.espcore.apps.affy.BirdSuite.run(BirdSuite.java:396)
... 1 more
Caused by: edu.mit.broad.mpgcore.exception.MPGRuntimeException: java.io.IOException: Cannot run program "/home/bhli/EXEDIR/cn_annotate_allele_summary": java.io.IOException: error=2, No such file or directory
at edu.mit.broad.espcore.apps.affy.BirdSuite.execWithStdOutputs(BirdSuite.java:359)
at edu.mit.broad.espcore.apps.affy.BirdSuite.annotate_allele_summaries(BirdSuite.java:478)
... 6 more
Caused by: java.io.IOException: Cannot run program "/home/bhli/EXEDIR/cn_annotate_allele_summary": java.io.IOException: error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at java.lang.Runtime.exec(Runtime.java:593)
at edu.mit.broad.espcore.apps.affy.BirdSuite.execWithStdOutputs(BirdSuite.java:335)
... 7 more
Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
at java.lang.ProcessImpl.start(ProcessImpl.java:65)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)


Sorry to jump on ya for something so trivial ... But it really does make it easier on people. Best of luck with finding your solution.

Last edited by Hevithan; 05-20-2011 at 09:13 PM.
 
  


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