BIRDSUITE error ["could not open 'GenomeWideSNP_6.birdsuite_probelist' to read".]

Question

[cruzpedro]

Hi folks,

I'm currently trying to use Birdsuite (http://www.broadinstitute.org/science/programs/medical-and-population-genetics/birdsuite/birdsuite-0) for CNV/SNP analysis and after installing it, I try to run like this:

/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/

But I am getting this message of error:

+ 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 Jun 04 09:43:13 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

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

Since there is no reference to that GenomeWideSNP_6.birdsuite_probelist in the software documentation, I believe that it should be created by the command above itself. Is there anyone who have used this software, and if not, who have the slightest clue what is going on? I a newbie in bioinformatics, so I apologize if that's too trivial.

Thanks,
Pedro.

[cruzpedro]

Sorry for the amoumt of tex