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Picard: "ERROR:INVALID_VERSION_NUMBER"

flescaiflescai Member Posts: 67 ✭✭

Hi guys,
probably my bad, but couldn't find in Picard Documentation an explanation of the error "ERROR:INVALID_VERSION_NUMBER"
Would someone be able to shed some light, and explain what such an error refers to, and if that is something I should worry about before processing samples through GATK?
cheers,
Francesco

Issue · Github
by Sheila

Issue Number
397
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
chandrans

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,184 admin

    What were you running when you encountered this error? A lot of errors are context dependent, so we can't help you without knowing more about what you were trying to do.

    Geraldine Van der Auwera, PhD

  • flescaiflescai Member Posts: 67 ✭✭

    Hi @Geraldine_VdAuwera,
    I was running HaplotypeCaller and I had some errors, pointing out to some truncated recalibrated bam files.

    I decided to be systematic, and run all my bams through Picard ValidateSamFile and which confirmed the truncation, but also reported that error for some of the other bams: they didn't generate any problem in GATK, but since I couldn't find an immediate explanation of what the error means I just thought better to ask before running again.

    These bam files are exome sequences, they have been aligned with the latest version of BWA, and there is no other particular characteristic that would distinguish them from the others that run just fine.

    I also checked the code of htsjdk/src/java/htsjdk/samtools/SAMValidationError.java
    but INVALID_VERSION_NUMBER seems to be one of the few errors without a comment.

    thanks,
    Francesco

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,184 admin

    Ok, with context it sounds like the error relates to the version indicated in the bam header. You can check what it is with samtools view -H. What software are you using to produce these bams?

    Geraldine Van der Auwera, PhD

  • flescaiflescai Member Posts: 67 ✭✭

    Hi @Geraldine_VdAuwera, thanks for following that up.
    They're produced with BWA 0.7.12-r1039

    the versions indicated in the header are

       @HD  VN:1.5  GO:none SO:coordinate
       @PG  ID:GATK IndelRealigner  VN:3.5-0-g36282e4
       @PG  ID:MarkDuplicates
       @PG  ID:bwa  PN:bwa  VN:0.7.12-r1039
       @PG  ID:GATK PrintReads  VN:3.5-0-g36282e4
    

    Should the error refer to the version of the software in PG lines or in the HD line?

    Issue · Github
    by Sheila

    Issue Number
    411
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    chandrans
  • SheilaSheila Broad InstituteMember, Broadie, Moderator, Dev Posts: 4,466 admin

    @flescai
    Hi Francesco,

    Which Picard version are you using? It seems you may have two options here. You can try upgrading to a newer version of Picard which will support more recent versions of the BAM specification. Or, you can try setting IGNORE=INVALID_VERSION_NUMBER in your command.

    -Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,184 admin

    You shouldn't use arguments to ignore validation unless you know for sure that it's going to be safe. Validation is important. If you run with a version of Picard that doesn't support the version of the spec that the file uses, you may run into problems later on and find you have wasted a whole bunch of time and compute.

    Geraldine Van der Auwera, PhD

  • flescaiflescai Member Posts: 67 ✭✭

    Hey @Sheila and and @Geraldine_VdAuwera
    thank you both for your answers. I couldn't use the very latest version (2.0.1) and used the 1.96 to run this validation.
    however, I also used the picard jar called from Queue, using the command

    'java'  '-Xmx2048m'  '-Djava.io.tmpdir=/faststorage/project/tmp'  \
    '-cp' '/com/extra/GATKQueue/3.5/jar-bin/Queue.jar'  \
    'picard.sam.ValidateSamFile'  \
    'INPUT=/faststorage/project/150.clean.dedup.recal.bam'  \
    'TMP_DIR=/faststorage/project/tmp'  \
    'MODE=SUMMARY' \
    'IGNORE_WARNINGS=true'
    

    I thought by doing so I would somehow make sure the validation is the same that GATK performs.

    However, apologies for asking more explicitly, could you please clarify when the error INVALID_VERSION_NUMBER is generated :smile: is that only related to compatibility between Picard version and Bam file version spec?
    so has that any relevance for processing the samples through GATK?

    cheers,
    Francesco

  • flescaiflescai Member Posts: 67 ✭✭

    thanks for the effort @Sheila very much appreciated!!

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