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Error while running GATK4 CNV workflow (something with the HDF5 lib)

xuejiaxuejia CrownbioMember

Hi the GATK team,
I am a new user of GATK4 CNV workflow. I always had an error while running the 3rd step NormalizeSomaticReadCounts:

16:08:11.670 INFO IntelGKLUtils - Trying to load Intel GKL library from:
jar:file:/home/jxue/softwares/GATK4_CNV/gatk4.jar!/com/intel/gkl/native/libIntelGKL.so
16:08:11.716 INFO IntelGKLUtils - Intel GKL library loaded from classpath.
[February 14, 2017 4:08:11 PM CST] org.broadinstitute.hellbender.tools.exome.NormalizeSomaticReadCounts --input E08055T.pcov.txt --panelOfNormals combined-normals.tsv --tangentNormalized E08055T.tn.tsv --preTangentNormalized E08055T.ptn.tsv --help false --version false --verbosity INFO --QUIET false --use_jdk_deflater false
[February 14, 2017 4:08:11 PM CST] Executing as [email protected] on Linux 2.6.32-431.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_112-b15; Version: Version:0288cff-SNAPSHOT
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.BUFFER_SIZE : 131072
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.COMPRESSION_LEVEL : 5
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.CREATE_INDEX : false
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.CREATE_MD5 : false
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.CUSTOM_READER_FACTORY :
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.EBI_REFERENCE_SERVICE_URL_MASK : http://www.ebi.ac.uk/ena/cram/md5/%s
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.NON_ZERO_BUFFER_SIZE : 131072
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.REFERENCE_FASTA : null
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:08:11.719 INFO NormalizeSomaticReadCounts - Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : false
16:08:11.720 INFO NormalizeSomaticReadCounts - Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:08:11.720 INFO NormalizeSomaticReadCounts - Defaults.USE_CRAM_REF_DOWNLOAD : false
16:08:11.720 INFO NormalizeSomaticReadCounts - Deflater IntelDeflater
16:08:11.720 INFO NormalizeSomaticReadCounts - Initializing engine
16:08:11.720 INFO NormalizeSomaticReadCounts - Done initializing engine
log4j:WARN No appenders could be found for logger (org.broadinstitute.hdf5.HDF5Library).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
#000: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5F.c line 604 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#001: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Fint.c line 1085 in H5F_open(): unable to read superblock
major: File accessibilty
minor: Read failed
#002: /mnt/scr1/abyrne/HDFJava-platypus-2.11/native/HDF5-prefix/src/HDF5/src/H5Fsuper.c line 277 in H5F_super_read(): file signature not found
major: File accessibilty
minor: Not an HDF5 file
16:08:11.775 INFO NormalizeSomaticReadCounts - Shutting down engine
[February 14, 2017 4:08:11 PM CST] org.broadinstitute.hellbender.tools.exome.NormalizeSomaticReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1465384960
org.broadinstitute.hdf5.HDF5LibException: exception when opening '/home/jxue/xue/CopywriteR/79WES_TandN/combined-normals.tsv' with READ_ONLY mode: Not an HDF5 file
at org.broadinstitute.hdf5.HDF5File.open(HDF5File.java:490)
at org.broadinstitute.hdf5.HDF5File.(HDF5File.java:82)
at org.broadinstitute.hdf5.HDF5File.(HDF5File.java:66)
at org.broadinstitute.hellbender.tools.exome.NormalizeSomaticReadCounts.doWork(NormalizeSomaticReadCounts.java:105)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:108)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:166)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:76)
at org.broadinstitute.hellbender.Main.main(Main.java:92)
Caused by: ncsa.hdf.hdf5lib.exceptions.HDF5FileInterfaceException: Not an HDF5 file
at ncsa.hdf.hdf5lib.H5._H5Fopen(Native Method)
at ncsa.hdf.hdf5lib.H5.H5Fopen(H5.java:2795)
at org.broadinstitute.hdf5.HDF5File.open(HDF5File.java:487)
... 8 more

I guess it should be the problem with HDF5 library.
Please reply as soon as possible. Thank you very much in advance!

Cheers,
Jia

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Best Answer

Answers

  • EADGEADG KielMember ✭✭✭

    Hi @xuejia,

    Iam not an expert for gatk4 CNV but after a short glance at your stack-trace I would say either your hdf5 file is corrupt or is not on the position you specified or there is a right/permission problem.

    major: File accessibilty
    minor: Unable to open file
    
    major: File accessibilty
    minor: Not an HDF5 file
    

    Can you check this ?

  • xuejiaxuejia CrownbioMember

    @EADG said:
    Hi @xuejia,

    Iam not an expert for gatk4 CNV but after a short glance at your stack-trace I would say either your hdf5 file is corrupt or is not on the position you specified or there is a right/permission problem.

    major: File accessibilty
    minor: Unable to open file
    
    major: File accessibilty
    minor: Not an HDF5 file
    

    Can you check this ?

    Thank you for your answer! I have no idea. I followed the instruction (http://depts.washington.edu/cssuwb/wiki/linux_hdf5_installation) to install HDF5 1.8.13 for my Redhat system. And then put HDF5-Java JNI Libraries Release 2.9 under "/usr/lib/jni/" as the tutorial (http://gatkforums.broadinstitute.org/gatk/discussion/6791/description-and-examples-of-the-steps-in-the-cnv-case-and-cnv-pon-creation-workflows#) described. Then gave the command to run the analysis:
    java -Djava.library.path=/usr/lib/jni/lib/linux/ -jar /home/jxue/softwares/GATK4_CNV/gatk4.jar NormalizeSomaticReadCounts -I E08055T.pcov.txt -PON combined-normals.tsv -PTN E08055T.ptn.tsv -TN E08055T.tn.tsv

    It always gives this error...
    Do you have any idea about this? It is more likely that I did not install HDF5 or HDF5-Java correctly.
    Thanks again!

    Jia

  • xuejiaxuejia CrownbioMember

    @EADG said:
    hm...crossreading over the tutorial i would say something went wrong with the creation of the PON.

    --panelOfNormals combined-normals.tsv
    

    The combined-normals.tsv is the file which you need in Step 2 (see the pdf in GoogleDrive) to create your PON.

    java -jar gatk4.jar CreatePanelOfNormals \
    
    -I sandbox/combined-normals.tsv \
    
    -O sandbox/normals.pon \
    
    -noQC \
    
    --disableSpark \
    
    --minimumTargetFactorPercentileThreshold 5
    

    Can you run the CreatePanelOfNormals again and put the result normals.pon into NormalizeSomaticReadCounts instead of combined-normals.tsv .

    java -jar gatk4.jar NormalizeSomaticReadCounts \
    
    -I cov/tumor.tsv \
    
    -PON sandbox/normals.pon \
    
    -PTN sandbox/tumor.ptn.tsv \
    
    -TN sandbox/tumor.tn.tsv
    

    By the way E08055T.pcov.txt should have the suffix tsv :)

    Hope this helps.

    Exactly! I missed one step before computing normalized read counts. Thank you very much for the help!
    But now I have another problem while plotting the results. I can get all the output files from Step 3,4 and 6 except the genome plots. All the read dots are missing in resulting PNG files. I can only see the axes and labels.

    I don't know if you can help.

    Thanks again!

    Jia
    imageimageimageimageimageimageimageimageimageimageimage

  • EADGEADG KielMember ✭✭✭

    hm can you check if all your outputfiles from the different steps have data in it? (open with nano/vim and check if more then the header is present)...or something went wrong with the installation of the r-packages (Rscript install_R_packages.R)... if this dont help, can you open a new thread ? Maybe other people can help...

  • xuejiaxuejia CrownbioMember

    @EADG said:
    hm can you check if all your outputfiles from the different steps have data in it? (open with nano/vim and check if more then the header is present)...or something went wrong with the installation of the r-packages (Rscript install_R_packages.R)... if this dont help, can you open a new thread ? Maybe other people can help...

    I check the outputs files. They all look fine. If it is someting with the R packages, I did not see any error message during this step.
    Thank you very much anyway. I will post a new question to others.

    Cheers,
    Jia

  • shleeshlee CambridgeMember, Broadie, Moderator admin

    Hi @xuejia,

    Please see if your issue is the same as that described here.

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