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Old 05-19-2011, 10:34 PM   #1
yimaizhe
LQ Newbie
 
Registered: May 2011
Posts: 11

Rep: Reputation: Disabled
A question about changing the scripts


I am intended to install the birdsuite(a genetics software used to detect CNV,SNP http://www.broadinstitute.org/scienc...dsuite-install) on ubuntu10.10

when comes to the last step:
# Edit birdsuite.sh, and add the following arguments to the java command line: --exeDir=EXEDIR --metadataDir=METADATADIR

I am a newer on linux,and I do not know where is the java command line and where should I add the arguments.
The birdsuite.sh is as follows:

#! /bin/bash
# The Broad Institute
# SOFTWARE COPYRIGHT NOTICE AGREEMENT
# This software and its documentation are copyright 2007 by the
# Broad Institute/Massachusetts Institute of Technology. All rights are
# reserved.

# This software is supplied without any warranty or guaranteed support
# whatsoever. Neither the Broad Institute nor MIT can be responsible for its
# use, misuse, or functionality.

set -e

# If --exeDir has been passed on the command line, it must be detected so that
# R_LIBS can be set correctly, in addition to passing --exeDir along to Birdsuite.jar.
# If --exeDir has not been passed on the command line, then by default the
# executables are found in the same directory as birdsuite.sh itself.

exedir=`dirname $0`
exedir_implicit=1

# This mess of punctuation iterates downward, because
# the command-line args go into BASH_ARGV backward.
# If --exeDir is the last argument on the command line, it is
# not detected here, but will cause Birdsuite.jar to fail.
for (( i=((${#BASH_ARGV[@]}-1)) ; i > 0 ; --i ))
do if [[ ${BASH_ARGV[$i]} == --exeDir ]]
then exedir=${BASH_ARGV[(($i-1))]}
exedir_implicit=''
fi
done

set -x

unset DISPLAY
export MCR_INHIBIT_CTF_LOCK=1
#experimental change for when python is packaged.
#PYTHONPATH=$PYTHONPATH:$exedir
#export PYTHONPATH
exedir=`${exedir}/getAbsPath ${exedir}`

# So that R can pick up broadgap packages
export R_LIBS=$exedir:$R_LIBS

if [ -n "$exedir_implicit" ]
then exedir_args="--exeDir=$exedir"
fi

java -jar $exedir/Birdsuite.jar $exedir_args $*


could you please help me to add the arguments ?
I have tried to add the arguments as follows,but all fail.

1> java -jar $exedir/Birdsuite.jar $exedir_args $* --exeDir=EXEDIR --metadataDir=METADATADIR

bhli@ubuntu:~/TESTDIR$ ~/EXEDIR/birdsuite.sh --basename=test --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=test.gender --celFiles=test.cels --noLsf --apt_probeset_summarize.force
+ 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 --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=test.gender --celFiles=test.cels --noLsf --apt_probeset_summarize.force --exeDir=EXEDIR --metadataDir=METADATADIR
Version File not found. Version checking disabled.
Fri May 20 09:45:18 CST 2011 Calling EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file METADATADIR/GenomeWideSNP_6.Full.cdf --probeset-ids 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
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 "EXEDIR/apt-probeset-summarize.sh": 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.apt_probeset_summarize(BirdSuite.java:466)
... 6 more
Caused by: java.io.IOException: Cannot run program "EXEDIR/apt-probeset-summarize.sh": 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, 04:49 PM   #2
jefro
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Registered: Mar 2008
Posts: 15,374

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I think I would have put this at the end of that line.

--exeDir=EXEDIR --metadataDir=METADATADIR
 
Old 05-28-2014, 04:45 PM   #3
soulsacros
LQ Newbie
 
Registered: May 2014
Posts: 2

Rep: Reputation: Disabled
I know that the thread is old by now, but I'm facing a similar problem. yimaizhe, could you find a solution?

That's what returns to me:

+ unset DISPLAY
+ export MCR_INHIBIT_CTF_LOCK=1
+ MCR_INHIBIT_CTF_LOCK=1
++ /home/pedro/Desktop/BIRDSUITE/EXEDIR/getAbsPath /home/pedro/Desktop/BIRDSUITE/EXEDIR
+ exedir=/home/pedro/Desktop/BIRDSUITE/EXEDIR
+ export R_LIBS=/home/pedro/Desktop/BIRDSUITE/EXEDIR:
+ R_LIBS=/home/pedro/Desktop/BIRDSUITE/EXEDIR:
+ '[' -n 1 ']'
+ exedir_args=--exeDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR
+ java -jar /home/pedro/Desktop/BIRDSUITE/EXEDIR/Birdsuite.jar --exeDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR --basename=BASE --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=AVC.gender --celFiles=AVC.cel --noLsf --apt_probeset_summarize.force --metadataDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/
Version File not found. Version checking disabled.
Wed May 28 17:25:41 BRT 2014 Calling /home/pedro/Desktop/BIRDSUITE/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/GenomeWideSNP_6.Full.cdf --probeset-ids /home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/GenomeWideSNP_6.birdsuite_probelist --mem-usage 4000 --block-size 0 --precision 2 --force ind32_(genomewidesnp_6).cel ind33_(genomewidesnp_6).cel ind34_(genomewidesnp_6).cel ind35_(genomewidesnp_6).cel ind36_(genomewidesnp_6).cel ind37_(genomewidesnp_6).cel ind38_(genomewidesnp_6).cel ind39_(genomewidesnp_6).cel ind28_(genomewidesnp_6).cel ind29_(genomewidesnp_6).cel ind30_(genomewidesnp_6).cel ind31_(genomewidesnp_6).cel ind2123082013_(genomewidesnp_6).cel ind2223082013_(genomewidesnp_6).cel ind2323082013_(genomewidesnp_6).cel ind2423082013_(genomewidesnp_6).cel ind2523082013_(genomewidesnp_6).cel ind2623082013_(genomewidesnp_6).cel ind2723082013_(genomewidesnp_6).cel ind8_(genomewidesnp_6).cel ind9_(genomewidesnp_6).cel ind10_(genomewidesnp_6).cel ind11_(genomewidesnp_6).cel ind12_(genomewidesnp_6).cel ind13_(genomewidesnp_6).cel ind1_(genomewidesnp_6).cel ind2_(genomewidesnp_6).cel ind3_(genomewidesnp_6).cel ind4_(genomewidesnp_6).cel ind5_(genomewidesnp_6).cel ind6_(genomewidesnp_6).cel ind7_(genomewidesnp_6).cel ind14311012_(genomewidesnp_6).cel ind15311012_(genomewidesnp_6).cel ind16311012_(genomewidesnp_6).cel ind17311012_(genomewidesnp_6).cel ind18311012_(genomewidesnp_6).cel ind19311012_(genomewidesnp_6).cel ind20311012_(genomewidesnp_6).cel b2.cel c2.cel d2.cel e2.cel 10c_(genomewidesnp_6).cel 10d05092011_(genomewidesnp_6).cel a1190411_(genomewidesnp_6).cel a04_(genomewidesnp_6).cel a613092011_(genomewidesnp_6).cel b04_(genomewidesnp_6).cel b613092011_(genomewidesnp_6).cel c113092011_(genomewidesnp_6)_2.cel c3190411_(genomewidesnp_6).cel c3_(genomewidesnp_6).cel c04_(genomewidesnp_6).cel c613092011_(genomewidesnp_6).cel c1013092011_(genomewidesnp_6).cel d113092011_(genomewidesnp_6).cel d04_(genomewidesnp_6).cel d4190411_(genomewidesnp_6).cel d4_(genomewidesnp_6).cel d613092011_(genomewidesnp_6).cel d1013092011_(genomewidesnp_6).cel e113092011_(genomewidesnp_6).cel e5190411_(genomewidesnp_6).cel e613092011_(genomewidesnp_6).cel f113092011_(genomewidesnp_6).cel f6190411_(genomewidesnp_6).cel f613092011_(genomewidesnp_6).cel g7190411_(genomewidesnp_6).cel h613092011_(genomewidesnp_6).cel 2b05092011_(genomewidesnp_6).cel 2c05092011_(genomewidesnp_6).cel 2d05092011_(genomewidesnp_6).cel 2e05092011_(genomewidesnp_6).cel a1160511_(genomewidesnp_6).cel b2160511_(genomewidesnp_6).cel c3160511_(genomewidesnp_6).cel d4160511_(genomewidesnp_6).cel e5160511_(genomewidesnp_6).cel e1013092011_(genomewidesnp_6).cel f6160511_(genomewidesnp_6).cel f1013092011_(genomewidesnp_6).cel 10b05092011_(genomewidesnp_6).cel b2190411_(genomewidesnp_6).cel g613092011_(genomewidesnp_6).cel

FATAL ERROR: TsvFile.cpp:2352: open: Could not open file: '/home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/GenomeWideSNP_6.birdsuite_probelist' to read.
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:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at edu.mit.broad.espcore.apps.affy.BirdSuite.run(BirdSuite.java:396)
... 1 more
Caused by: edu.mit.broad.mpgcore.exception.MPGRuntimeException: Non-zero exit status: 1 from command '/home/pedro/Desktop/BIRDSUITE/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/GenomeWideSNP_6.Full.cdf --probeset-ids /home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/GenomeWideSNP_6.birdsuite_probelist --mem-usage 4000 --block-size 0 --precision 2 --force ind32_(genomewidesnp_6).cel ind33_(genomewidesnp_6).cel ind34_(genomewidesnp_6).cel ind35_(genomewidesnp_6).cel ind36_(genomewidesnp_6).cel ind37_(genomewidesnp_6).cel ind38_(genomewidesnp_6).cel ind39_(genomewidesnp_6).cel ind28_(genomewidesnp_6).cel ind29_(genomewidesnp_6).cel ind30_(genomewidesnp_6).cel ind31_(genomewidesnp_6).cel ind2123082013_(genomewidesnp_6).cel ind2223082013_(genomewidesnp_6).cel ind2323082013_(genomewidesnp_6).cel ind2423082013_(genomewidesnp_6).cel ind2523082013_(genomewidesnp_6).cel ind2623082013_(genomewidesnp_6).cel ind2723082013_(genomewidesnp_6).cel ind8_(genomewidesnp_6).cel ind9_(genomewidesnp_6).cel ind10_(genomewidesnp_6).cel ind11_(genomewidesnp_6).cel ind12_(genomewidesnp_6).cel ind13_(genomewidesnp_6).cel ind1_(genomewidesnp_6).cel ind2_(genomewidesnp_6).cel ind3_(genomewidesnp_6).cel ind4_(genomewidesnp_6).cel ind5_(genomewidesnp_6).cel ind6_(genomewidesnp_6).cel ind7_(genomewidesnp_6).cel ind14311012_(genomewidesnp_6).cel ind15311012_(genomewidesnp_6).cel ind16311012_(genomewidesnp_6).cel ind17311012_(genomewidesnp_6).cel ind18311012_(genomewidesnp_6).cel ind19311012_(genomewidesnp_6).cel ind20311012_(genomewidesnp_6).cel b2.cel c2.cel d2.cel e2.cel 10c_(genomewidesnp_6).cel 10d05092011_(genomewidesnp_6).cel a1190411_(genomewidesnp_6).cel a04_(genomewidesnp_6).cel a613092011_(genomewidesnp_6).cel b04_(genomewidesnp_6).cel b613092011_(genomewidesnp_6).cel c113092011_(genomewidesnp_6)_2.cel c3190411_(genomewidesnp_6).cel c3_(genomewidesnp_6).cel c04_(genomewidesnp_6).cel c613092011_(genomewidesnp_6).cel c1013092011_(genomewidesnp_6).cel d113092011_(genomewidesnp_6).cel d04_(genomewidesnp_6).cel d4190411_(genomewidesnp_6).cel d4_(genomewidesnp_6).cel d613092011_(genomewidesnp_6).cel d1013092011_(genomewidesnp_6).cel e113092011_(genomewidesnp_6).cel e5190411_(genomewidesnp_6).cel e613092011_(genomewidesnp_6).cel f113092011_(genomewidesnp_6).cel f6190411_(genomewidesnp_6).cel f613092011_(genomewidesnp_6).cel g7190411_(genomewidesnp_6).cel h613092011_(genomewidesnp_6).cel 2b05092011_(genomewidesnp_6).cel 2c05092011_(genomewidesnp_6).cel 2d05092011_(genomewidesnp_6).cel 2e05092011_(genomewidesnp_6).cel a1160511_(genomewidesnp_6).cel b2160511_(genomewidesnp_6).cel c3160511_(genomewidesnp_6).cel d4160511_(genomewidesnp_6).cel e5160511_(genomewidesnp_6).cel e1013092011_(genomewidesnp_6).cel f6160511_(genomewidesnp_6).cel f1013092011_(genomewidesnp_6).cel 10b05092011_(genomewidesnp_6).cel b2190411_(genomewidesnp_6).cel g613092011_(genomewidesnp_6).cel'
at edu.mit.broad.espcore.apps.affy.BirdSuite.execWithStdOutputs(BirdSuite.java:353)
at edu.mit.broad.espcore.apps.affy.BirdSuite.apt_probeset_summarize(BirdSuite.java:466)
... 6 more
root@pedro-VirtualBox:/home/pedro/Desktop/BIRDSUITE/EXEDIR/TESTDIR# /home/pedro/Desktop/BIRDSUITE/EXEDIR/birdsuite.sh --basename=AVC --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=AVC.gender --celFiles=AVC.cel --noLsf --apt_probeset_summarize.force --metadataDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR/
+ unset DISPLAY
+ export MCR_INHIBIT_CTF_LOCK=1
+ MCR_INHIBIT_CTF_LOCK=1
++ /home/pedro/Desktop/BIRDSUITE/EXEDIR/getAbsPath /home/pedro/Desktop/BIRDSUITE/EXEDIR
+ exedir=/home/pedro/Desktop/BIRDSUITE/EXEDIR
+ export R_LIBS=/home/pedro/Desktop/BIRDSUITE/EXEDIR:
+ R_LIBS=/home/pedro/Desktop/BIRDSUITE/EXEDIR:
+ '[' -n 1 ']'
+ exedir_args=--exeDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR
+ java -jar /home/pedro/Desktop/BIRDSUITE/EXEDIR/Birdsuite.jar --exeDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR --basename=AVC --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=AVC.gender --celFiles=AVC.cel --noLsf --apt_probeset_summarize.force --metadataDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR/
Version File not found. Version checking disabled.
Wed May 28 17:31:28 BRT 2014 Calling /home/pedro/Desktop/BIRDSUITE/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /home/pedro/Desktop/BIRDSUITE/EXEDIR/GenomeWideSNP_6.Full.cdf --probeset-ids /home/pedro/Desktop/BIRDSUITE/EXEDIR/GenomeWideSNP_6.birdsuite_probelist --mem-usage 4000 --block-size 0 --precision 2 --force ind32_(genomewidesnp_6).cel ind33_(genomewidesnp_6).cel ind34_(genomewidesnp_6).cel ind35_(genomewidesnp_6).cel ind36_(genomewidesnp_6).cel ind37_(genomewidesnp_6).cel ind38_(genomewidesnp_6).cel ind39_(genomewidesnp_6).cel ind28_(genomewidesnp_6).cel ind29_(genomewidesnp_6).cel ind30_(genomewidesnp_6).cel ind31_(genomewidesnp_6).cel ind2123082013_(genomewidesnp_6).cel ind2223082013_(genomewidesnp_6).cel ind2323082013_(genomewidesnp_6).cel ind2423082013_(genomewidesnp_6).cel ind2523082013_(genomewidesnp_6).cel ind2623082013_(genomewidesnp_6).cel ind2723082013_(genomewidesnp_6).cel ind8_(genomewidesnp_6).cel ind9_(genomewidesnp_6).cel ind10_(genomewidesnp_6).cel ind11_(genomewidesnp_6).cel ind12_(genomewidesnp_6).cel ind13_(genomewidesnp_6).cel ind1_(genomewidesnp_6).cel ind2_(genomewidesnp_6).cel ind3_(genomewidesnp_6).cel ind4_(genomewidesnp_6).cel ind5_(genomewidesnp_6).cel ind6_(genomewidesnp_6).cel ind7_(genomewidesnp_6).cel ind14311012_(genomewidesnp_6).cel ind15311012_(genomewidesnp_6).cel ind16311012_(genomewidesnp_6).cel ind17311012_(genomewidesnp_6).cel ind18311012_(genomewidesnp_6).cel ind19311012_(genomewidesnp_6).cel ind20311012_(genomewidesnp_6).cel b2.cel c2.cel d2.cel e2.cel 10c_(genomewidesnp_6).cel 10d05092011_(genomewidesnp_6).cel a1190411_(genomewidesnp_6).cel a04_(genomewidesnp_6).cel a613092011_(genomewidesnp_6).cel b04_(genomewidesnp_6).cel b613092011_(genomewidesnp_6).cel c113092011_(genomewidesnp_6)_2.cel c3190411_(genomewidesnp_6).cel c3_(genomewidesnp_6).cel c04_(genomewidesnp_6).cel c613092011_(genomewidesnp_6).cel c1013092011_(genomewidesnp_6).cel d113092011_(genomewidesnp_6).cel d04_(genomewidesnp_6).cel d4190411_(genomewidesnp_6).cel d4_(genomewidesnp_6).cel d613092011_(genomewidesnp_6).cel d1013092011_(genomewidesnp_6).cel e113092011_(genomewidesnp_6).cel e5190411_(genomewidesnp_6).cel e613092011_(genomewidesnp_6).cel f113092011_(genomewidesnp_6).cel f6190411_(genomewidesnp_6).cel f613092011_(genomewidesnp_6).cel g7190411_(genomewidesnp_6).cel h613092011_(genomewidesnp_6).cel 2b05092011_(genomewidesnp_6).cel 2c05092011_(genomewidesnp_6).cel 2d05092011_(genomewidesnp_6).cel 2e05092011_(genomewidesnp_6).cel a1160511_(genomewidesnp_6).cel b2160511_(genomewidesnp_6).cel c3160511_(genomewidesnp_6).cel d4160511_(genomewidesnp_6).cel e5160511_(genomewidesnp_6).cel e1013092011_(genomewidesnp_6).cel f6160511_(genomewidesnp_6).cel f1013092011_(genomewidesnp_6).cel 10b05092011_(genomewidesnp_6).cel b2190411_(genomewidesnp_6).cel g613092011_(genomewidesnp_6).cel

FATAL ERROR: EngineUtil::getCdfChipType() - Can't read header for /home/pedro/Desktop/BIRDSUITE/EXEDIR/GenomeWideSNP_6.Full.cdf. Description: Unable to open the file.
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:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at edu.mit.broad.espcore.apps.affy.BirdSuite.run(BirdSuite.java:396)
... 1 more
Caused by: edu.mit.broad.mpgcore.exception.MPGRuntimeException: Non-zero exit status: 1 from command '/home/pedro/Desktop/BIRDSUITE/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /home/pedro/Desktop/BIRDSUITE/EXEDIR/GenomeWideSNP_6.Full.cdf --probeset-ids /home/pedro/Desktop/BIRDSUITE/EXEDIR/GenomeWideSNP_6.birdsuite_probelist --mem-usage 4000 --block-size 0 --precision 2 --force ind32_(genomewidesnp_6).cel ind33_(genomewidesnp_6).cel ind34_(genomewidesnp_6).cel ind35_(genomewidesnp_6).cel ind36_(genomewidesnp_6).cel ind37_(genomewidesnp_6).cel ind38_(genomewidesnp_6).cel ind39_(genomewidesnp_6).cel ind28_(genomewidesnp_6).cel ind29_(genomewidesnp_6).cel ind30_(genomewidesnp_6).cel ind31_(genomewidesnp_6).cel ind2123082013_(genomewidesnp_6).cel ind2223082013_(genomewidesnp_6).cel ind2323082013_(genomewidesnp_6).cel ind2423082013_(genomewidesnp_6).cel ind2523082013_(genomewidesnp_6).cel ind2623082013_(genomewidesnp_6).cel ind2723082013_(genomewidesnp_6).cel ind8_(genomewidesnp_6).cel ind9_(genomewidesnp_6).cel ind10_(genomewidesnp_6).cel ind11_(genomewidesnp_6).cel ind12_(genomewidesnp_6).cel ind13_(genomewidesnp_6).cel ind1_(genomewidesnp_6).cel ind2_(genomewidesnp_6).cel ind3_(genomewidesnp_6).cel ind4_(genomewidesnp_6).cel ind5_(genomewidesnp_6).cel ind6_(genomewidesnp_6).cel ind7_(genomewidesnp_6).cel ind14311012_(genomewidesnp_6).cel ind15311012_(genomewidesnp_6).cel ind16311012_(genomewidesnp_6).cel ind17311012_(genomewidesnp_6).cel ind18311012_(genomewidesnp_6).cel ind19311012_(genomewidesnp_6).cel ind20311012_(genomewidesnp_6).cel b2.cel c2.cel d2.cel e2.cel 10c_(genomewidesnp_6).cel 10d05092011_(genomewidesnp_6).cel a1190411_(genomewidesnp_6).cel a04_(genomewidesnp_6).cel a613092011_(genomewidesnp_6).cel b04_(genomewidesnp_6).cel b613092011_(genomewidesnp_6).cel c113092011_(genomewidesnp_6)_2.cel c3190411_(genomewidesnp_6).cel c3_(genomewidesnp_6).cel c04_(genomewidesnp_6).cel c613092011_(genomewidesnp_6).cel c1013092011_(genomewidesnp_6).cel d113092011_(genomewidesnp_6).cel d04_(genomewidesnp_6).cel d4190411_(genomewidesnp_6).cel d4_(genomewidesnp_6).cel d613092011_(genomewidesnp_6).cel d1013092011_(genomewidesnp_6).cel e113092011_(genomewidesnp_6).cel e5190411_(genomewidesnp_6).cel e613092011_(genomewidesnp_6).cel f113092011_(genomewidesnp_6).cel f6190411_(genomewidesnp_6).cel f613092011_(genomewidesnp_6).cel g7190411_(genomewidesnp_6).cel h613092011_(genomewidesnp_6).cel 2b05092011_(genomewidesnp_6).cel 2c05092011_(genomewidesnp_6).cel 2d05092011_(genomewidesnp_6).cel 2e05092011_(genomewidesnp_6).cel a1160511_(genomewidesnp_6).cel b2160511_(genomewidesnp_6).cel c3160511_(genomewidesnp_6).cel d4160511_(genomewidesnp_6).cel e5160511_(genomewidesnp_6).cel e1013092011_(genomewidesnp_6).cel f6160511_(genomewidesnp_6).cel f1013092011_(genomewidesnp_6).cel 10b05092011_(genomewidesnp_6).cel b2190411_(genomewidesnp_6).cel g613092011_(genomewidesnp_6).cel'
at edu.mit.broad.espcore.apps.affy.BirdSuite.execWithStdOutputs(BirdSuite.java:353)
at edu.mit.broad.espcore.apps.affy.BirdSuite.apt_probeset_summarize(BirdSuite.java:466)
... 6 more
root@pedro-VirtualBox:/home/pedro/Desktop/BIRDSUITE/EXEDIR/TESTDIR# /home/pedro/Desktop/BIRDSUITE/EXEDIR/birdsuite.sh --basename=AVC --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=AVC.gender --celFiles=AVC.cel --noLsf --apt_probeset_summarize.force --exeDir=EXEDIR --metadataDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR/
+ unset DISPLAY
+ export MCR_INHIBIT_CTF_LOCK=1
+ MCR_INHIBIT_CTF_LOCK=1
++ /home/pedro/Desktop/BIRDSUITE/EXEDIR/getAbsPath /home/pedro/Desktop/BIRDSUITE/EXEDIR
+ exedir=/home/pedro/Desktop/BIRDSUITE/EXEDIR
+ export R_LIBS=/home/pedro/Desktop/BIRDSUITE/EXEDIR:
+ R_LIBS=/home/pedro/Desktop/BIRDSUITE/EXEDIR:
+ '[' -n 1 ']'
+ exedir_args=--exeDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR
+ java -jar /home/pedro/Desktop/BIRDSUITE/EXEDIR/Birdsuite.jar --exeDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR --basename=AVC --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=AVC.gender --celFiles=AVC.cel --noLsf --apt_probeset_summarize.force --exeDir=EXEDIR --metadataDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR/
Version File not found. Version checking disabled.
Wed May 28 17:36:44 BRT 2014 Calling EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /home/pedro/Desktop/BIRDSUITE/EXEDIR/GenomeWideSNP_6.Full.cdf --probeset-ids /home/pedro/Desktop/BIRDSUITE/EXEDIR/GenomeWideSNP_6.birdsuite_probelist --mem-usage 4000 --block-size 0 --precision 2 --force ind32_(genomewidesnp_6).cel ind33_(genomewidesnp_6).cel ind34_(genomewidesnp_6).cel ind35_(genomewidesnp_6).cel ind36_(genomewidesnp_6).cel ind37_(genomewidesnp_6).cel ind38_(genomewidesnp_6).cel ind39_(genomewidesnp_6).cel ind28_(genomewidesnp_6).cel ind29_(genomewidesnp_6).cel ind30_(genomewidesnp_6).cel ind31_(genomewidesnp_6).cel ind2123082013_(genomewidesnp_6).cel ind2223082013_(genomewidesnp_6).cel ind2323082013_(genomewidesnp_6).cel ind2423082013_(genomewidesnp_6).cel ind2523082013_(genomewidesnp_6).cel ind2623082013_(genomewidesnp_6).cel ind2723082013_(genomewidesnp_6).cel ind8_(genomewidesnp_6).cel ind9_(genomewidesnp_6).cel ind10_(genomewidesnp_6).cel ind11_(genomewidesnp_6).cel ind12_(genomewidesnp_6).cel ind13_(genomewidesnp_6).cel ind1_(genomewidesnp_6).cel ind2_(genomewidesnp_6).cel ind3_(genomewidesnp_6).cel ind4_(genomewidesnp_6).cel ind5_(genomewidesnp_6).cel ind6_(genomewidesnp_6).cel ind7_(genomewidesnp_6).cel ind14311012_(genomewidesnp_6).cel ind15311012_(genomewidesnp_6).cel ind16311012_(genomewidesnp_6).cel ind17311012_(genomewidesnp_6).cel ind18311012_(genomewidesnp_6).cel ind19311012_(genomewidesnp_6).cel ind20311012_(genomewidesnp_6).cel b2.cel c2.cel d2.cel e2.cel 10c_(genomewidesnp_6).cel 10d05092011_(genomewidesnp_6).cel a1190411_(genomewidesnp_6).cel a04_(genomewidesnp_6).cel a613092011_(genomewidesnp_6).cel b04_(genomewidesnp_6).cel b613092011_(genomewidesnp_6).cel c113092011_(genomewidesnp_6)_2.cel c3190411_(genomewidesnp_6).cel c3_(genomewidesnp_6).cel c04_(genomewidesnp_6).cel c613092011_(genomewidesnp_6).cel c1013092011_(genomewidesnp_6).cel d113092011_(genomewidesnp_6).cel d04_(genomewidesnp_6).cel d4190411_(genomewidesnp_6).cel d4_(genomewidesnp_6).cel d613092011_(genomewidesnp_6).cel d1013092011_(genomewidesnp_6).cel e113092011_(genomewidesnp_6).cel e5190411_(genomewidesnp_6).cel e613092011_(genomewidesnp_6).cel f113092011_(genomewidesnp_6).cel f6190411_(genomewidesnp_6).cel f613092011_(genomewidesnp_6).cel g7190411_(genomewidesnp_6).cel h613092011_(genomewidesnp_6).cel 2b05092011_(genomewidesnp_6).cel 2c05092011_(genomewidesnp_6).cel 2d05092011_(genomewidesnp_6).cel 2e05092011_(genomewidesnp_6).cel a1160511_(genomewidesnp_6).cel b2160511_(genomewidesnp_6).cel c3160511_(genomewidesnp_6).cel d4160511_(genomewidesnp_6).cel e5160511_(genomewidesnp_6).cel e1013092011_(genomewidesnp_6).cel f6160511_(genomewidesnp_6).cel f1013092011_(genomewidesnp_6).cel 10b05092011_(genomewidesnp_6).cel b2190411_(genomewidesnp_6).cel g613092011_(genomewidesnp_6).cel
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:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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 "EXEDIR/apt-probeset-summarize.sh": 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.apt_probeset_summarize(BirdSuite.java:466)
... 6 more
Caused by: java.io.IOException: Cannot run program "EXEDIR/apt-probeset-summarize.sh": error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1041)
at java.lang.Runtime.exec(Runtime.java:617)
at edu.mit.broad.espcore.apps.affy.BirdSuite.execWithStdOutputs(BirdSuite.java:335)
... 7 more
Caused by: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.forkAndExec(Native Method)
at java.lang.UNIXProcess.<init>(UNIXProcess.java:186)
at java.lang.ProcessImpl.start(ProcessImpl.java:130)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1022)
... 9 more
root@pedro-VirtualBox:/home/pedro/Desktop/BIRDSUITE/EXEDIR/TESTDIR# /home/pedro/Desktop/BIRDSUITE/EXEDIR/birdsuite.sh --basename=AVC --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=AVC.gender --celFiles=AVC.cel --noLsf --apt_probeset_summarize.force --exeDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR --metadataDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/
+ unset DISPLAY
+ export MCR_INHIBIT_CTF_LOCK=1
+ MCR_INHIBIT_CTF_LOCK=1
++ /home/pedro/Desktop/BIRDSUITE/EXEDIR/getAbsPath /home/pedro/Desktop/BIRDSUITE/EXEDIR
+ exedir=/home/pedro/Desktop/BIRDSUITE/EXEDIR
+ export R_LIBS=/home/pedro/Desktop/BIRDSUITE/EXEDIR:
+ R_LIBS=/home/pedro/Desktop/BIRDSUITE/EXEDIR:
+ '[' -n 1 ']'
+ exedir_args=--exeDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR
+ java -jar /home/pedro/Desktop/BIRDSUITE/EXEDIR/Birdsuite.jar --exeDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR --basename=AVC --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=AVC.gender --celFiles=AVC.cel --noLsf --apt_probeset_summarize.force --exeDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR --metadataDir=/home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/
Version File not found. Version checking disabled.
Wed May 28 17:37:11 BRT 2014 Calling /home/pedro/Desktop/BIRDSUITE/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/GenomeWideSNP_6.Full.cdf --probeset-ids /home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/GenomeWideSNP_6.birdsuite_probelist --mem-usage 4000 --block-size 0 --precision 2 --force ind32_(genomewidesnp_6).cel ind33_(genomewidesnp_6).cel ind34_(genomewidesnp_6).cel ind35_(genomewidesnp_6).cel ind36_(genomewidesnp_6).cel ind37_(genomewidesnp_6).cel ind38_(genomewidesnp_6).cel ind39_(genomewidesnp_6).cel ind28_(genomewidesnp_6).cel ind29_(genomewidesnp_6).cel ind30_(genomewidesnp_6).cel ind31_(genomewidesnp_6).cel ind2123082013_(genomewidesnp_6).cel ind2223082013_(genomewidesnp_6).cel ind2323082013_(genomewidesnp_6).cel ind2423082013_(genomewidesnp_6).cel ind2523082013_(genomewidesnp_6).cel ind2623082013_(genomewidesnp_6).cel ind2723082013_(genomewidesnp_6).cel ind8_(genomewidesnp_6).cel ind9_(genomewidesnp_6).cel ind10_(genomewidesnp_6).cel ind11_(genomewidesnp_6).cel ind12_(genomewidesnp_6).cel ind13_(genomewidesnp_6).cel ind1_(genomewidesnp_6).cel ind2_(genomewidesnp_6).cel ind3_(genomewidesnp_6).cel ind4_(genomewidesnp_6).cel ind5_(genomewidesnp_6).cel ind6_(genomewidesnp_6).cel ind7_(genomewidesnp_6).cel ind14311012_(genomewidesnp_6).cel ind15311012_(genomewidesnp_6).cel ind16311012_(genomewidesnp_6).cel ind17311012_(genomewidesnp_6).cel ind18311012_(genomewidesnp_6).cel ind19311012_(genomewidesnp_6).cel ind20311012_(genomewidesnp_6).cel b2.cel c2.cel d2.cel e2.cel 10c_(genomewidesnp_6).cel 10d05092011_(genomewidesnp_6).cel a1190411_(genomewidesnp_6).cel a04_(genomewidesnp_6).cel a613092011_(genomewidesnp_6).cel b04_(genomewidesnp_6).cel b613092011_(genomewidesnp_6).cel c113092011_(genomewidesnp_6)_2.cel c3190411_(genomewidesnp_6).cel c3_(genomewidesnp_6).cel c04_(genomewidesnp_6).cel c613092011_(genomewidesnp_6).cel c1013092011_(genomewidesnp_6).cel d113092011_(genomewidesnp_6).cel d04_(genomewidesnp_6).cel d4190411_(genomewidesnp_6).cel d4_(genomewidesnp_6).cel d613092011_(genomewidesnp_6).cel d1013092011_(genomewidesnp_6).cel e113092011_(genomewidesnp_6).cel e5190411_(genomewidesnp_6).cel e613092011_(genomewidesnp_6).cel f113092011_(genomewidesnp_6).cel f6190411_(genomewidesnp_6).cel f613092011_(genomewidesnp_6).cel g7190411_(genomewidesnp_6).cel h613092011_(genomewidesnp_6).cel 2b05092011_(genomewidesnp_6).cel 2c05092011_(genomewidesnp_6).cel 2d05092011_(genomewidesnp_6).cel 2e05092011_(genomewidesnp_6).cel a1160511_(genomewidesnp_6).cel b2160511_(genomewidesnp_6).cel c3160511_(genomewidesnp_6).cel d4160511_(genomewidesnp_6).cel e5160511_(genomewidesnp_6).cel e1013092011_(genomewidesnp_6).cel f6160511_(genomewidesnp_6).cel f1013092011_(genomewidesnp_6).cel 10b05092011_(genomewidesnp_6).cel b2190411_(genomewidesnp_6).cel g613092011_(genomewidesnp_6).cel

FATAL ERROR: TsvFile.cpp:2352: open: Could not open file: '/home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/GenomeWideSNP_6.birdsuite_probelist' to read.
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:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at edu.mit.broad.espcore.apps.affy.BirdSuite.run(BirdSuite.java:396)
... 1 more
Caused by: edu.mit.broad.mpgcore.exception.MPGRuntimeException: Non-zero exit status: 1 from command '/home/pedro/Desktop/BIRDSUITE/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/GenomeWideSNP_6.Full.cdf --probeset-ids /home/pedro/Desktop/BIRDSUITE/EXEDIR/METADATADIR/GenomeWideSNP_6.birdsuite_probelist --mem-usage 4000 --block-size 0 --precision 2 --force ind32_(genomewidesnp_6).cel ind33_(genomewidesnp_6).cel ind34_(genomewidesnp_6).cel ind35_(genomewidesnp_6).cel ind36_(genomewidesnp_6).cel ind37_(genomewidesnp_6).cel ind38_(genomewidesnp_6).cel ind39_(genomewidesnp_6).cel ind28_(genomewidesnp_6).cel ind29_(genomewidesnp_6).cel ind30_(genomewidesnp_6).cel ind31_(genomewidesnp_6).cel ind2123082013_(genomewidesnp_6).cel ind2223082013_(genomewidesnp_6).cel ind2323082013_(genomewidesnp_6).cel ind2423082013_(genomewidesnp_6).cel ind2523082013_(genomewidesnp_6).cel ind2623082013_(genomewidesnp_6).cel ind2723082013_(genomewidesnp_6).cel ind8_(genomewidesnp_6).cel ind9_(genomewidesnp_6).cel ind10_(genomewidesnp_6).cel ind11_(genomewidesnp_6).cel ind12_(genomewidesnp_6).cel ind13_(genomewidesnp_6).cel ind1_(genomewidesnp_6).cel ind2_(genomewidesnp_6).cel ind3_(genomewidesnp_6).cel ind4_(genomewidesnp_6).cel ind5_(genomewidesnp_6).cel ind6_(genomewidesnp_6).cel ind7_(genomewidesnp_6).cel ind14311012_(genomewidesnp_6).cel ind15311012_(genomewidesnp_6).cel ind16311012_(genomewidesnp_6).cel ind17311012_(genomewidesnp_6).cel ind18311012_(genomewidesnp_6).cel ind19311012_(genomewidesnp_6).cel ind20311012_(genomewidesnp_6).cel b2.cel c2.cel d2.cel e2.cel 10c_(genomewidesnp_6).cel 10d05092011_(genomewidesnp_6).cel a1190411_(genomewidesnp_6).cel a04_(genomewidesnp_6).cel a613092011_(genomewidesnp_6).cel b04_(genomewidesnp_6).cel b613092011_(genomewidesnp_6).cel c113092011_(genomewidesnp_6)_2.cel c3190411_(genomewidesnp_6).cel c3_(genomewidesnp_6).cel c04_(genomewidesnp_6).cel c613092011_(genomewidesnp_6).cel c1013092011_(genomewidesnp_6).cel d113092011_(genomewidesnp_6).cel d04_(genomewidesnp_6).cel d4190411_(genomewidesnp_6).cel d4_(genomewidesnp_6).cel d613092011_(genomewidesnp_6).cel d1013092011_(genomewidesnp_6).cel e113092011_(genomewidesnp_6).cel e5190411_(genomewidesnp_6).cel e613092011_(genomewidesnp_6).cel f113092011_(genomewidesnp_6).cel f6190411_(genomewidesnp_6).cel f613092011_(genomewidesnp_6).cel g7190411_(genomewidesnp_6).cel h613092011_(genomewidesnp_6).cel 2b05092011_(genomewidesnp_6).cel 2c05092011_(genomewidesnp_6).cel 2d05092011_(genomewidesnp_6).cel 2e05092011_(genomewidesnp_6).cel a1160511_(genomewidesnp_6).cel b2160511_(genomewidesnp_6).cel c3160511_(genomewidesnp_6).cel d4160511_(genomewidesnp_6).cel e5160511_(genomewidesnp_6).cel e1013092011_(genomewidesnp_6).cel f6160511_(genomewidesnp_6).cel f1013092011_(genomewidesnp_6).cel 10b05092011_(genomewidesnp_6).cel b2190411_(genomewidesnp_6).cel g613092011_(genomewidesnp_6).cel'
at edu.mit.broad.espcore.apps.affy.BirdSuite.execWithStdOutputs(BirdSuite.java:353)
at edu.mit.broad.espcore.apps.affy.BirdSuite.apt_probeset_summarize(BirdSuite.java:466)
... 6 more
 
  


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