erro came out during the installation of Birdsuite

Question

[Taylor95]

Hi all, I am trying to install Birdsuite version-1.5.5. After installing the software following the instructions list on the web, I run the test command and got the error in the log:

 [taylor@jm 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
++ ../EXEDIR/getAbsPath ../EXEDIR
 + exedir=/dt3/lyq/birdsuite/EXEDIR
 + export R_LIBS=/dt3/lyq/birdsuite/EXEDIR:
 + R_LIBS=/dt3/lyq/birdsuite/EXEDIR:
 + '[' -n 1 ']'
 + exedir_args=--exeDir=/dt3/lyq/birdsuite/EXEDIR
 + java -jar /dt3/lyq/birdsuite/EXEDIR/Birdsuite.jar --exeDir=/dt3/lyq/birdsuite/EXEDIR --basename=test --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=test.gender --celFiles=test.cels --noLsf --apt_probeset_summarize.force --exeDir=/dt3/lyq/birdsuite/EXEDIR --metadataDir=/dt3/lyq/birdsuite/METADATADIR
Could not reach web site to check version
Wed Mar 27 11:03:07 CST 2019 Calling /dt3/lyq/birdsuite/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /dt3/lyq/birdsuite/METADATADIR/GenomeWideSNP_6.Full.cdf --probeset-ids /dt3/lyq/birdsuite/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

FATAL ERROR: Can't make or write to directory: output
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:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    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 '/dt3/lyq/birdsuite/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /dt3/lyq/birdsuite/METADATADIR/GenomeWideSNP_6.Full.cdf --probeset-ids /dt3/lyq/birdsuite/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'
    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

May this happen due to the link of web site or something else? I am new to the LINUX system and not familiar with java. Anybody can help me solve this or install birdsuite? Thanks in advance!

[Joe]

A couple of guesses, though I’m not familiar with the tool:

• Does the directory output have to exist first? It says it cannot make or write to it so I suspect this isn’t the problem, but worth checking.

• Do you have permissions to create directories in the current working directory? It may have failed to write/make dirs if the permissions are wrong.

• Try specifying a full output directory path, e.g. ~/outputdir/

[Taylor95]

The output directory has been made. I tried your advice to specify the full directory path but got the same erro.

[Kevin Blighe]

I am familiar with Birdsuite and the Birdseed algorithm. However, if you are only aiming to genotype your SNP 6.0 CEL files, then you may instead try the Genotyping Console:

• https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/genotyping-console-software.html

[Taylor95]

Can this software do the CNV calling from affy6.0 CEL files?

[Kevin Blighe]

Birdsuite? - it should, provided it is this that you are using: https://www.broadinstitute.org/birdsuite/birdsuite

You may want to contact them at the email address on the website.

The Genotyping Console, I believe, may only do the SNP calling - not 100% sure. When Affymetrix were acquired by ThermoFisher, I think that support for certain areas / teams was lost, including the Genotyping Console.

There are other programmatic ways to do copy number, too; You could look up 'Aroma Affymetrix' and you'll find it.

[Taylor95]

I have emailed them for the erro about installing Birdsuite but not heard back yet. I read some papers and foud that Birdsuite is one of the most frequently used softwares to call CNVs from SNP data. Do you know why the erro come out? Would you please help me solve this?

[Joe]

Without more information about your full install process, it might be impossible for use to diagnose this. If there was an error you missed in an earlier step for example, we won't know that.

[Taylor95]

I almost exactly followed the instruction on the website: https://www.broadinstitute.org/birdsuite/birdsuite-install

Except when I ran the Step5, an error "a 'NAMESPACE' file is required" would come out. Then I tried the code

tar -xzf broadgap.utils_1.0.tar.gz
cd broadgap.utils
echo 'exportPattern( "." )' > NAMESPACE
cd ..
tar -zcf broadgap.utils_1.0.tar.gz broadgap.utils`

and Step3:

easy_install --install-dir=/dt3/taylor/birdsuite/EXEDIR --script-dir=./ birdsuite-1.0-py2.5.egg

easy_install --install-dir=/dt3/taylor/birdsuite/EXEDIR --script-dir=./ mpgutils-0.7-py2.5.egg

[anamaria]

Hi Taylor

did you manage to install this and which version of R did you use?