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# Picard: "ERROR:INVALID_VERSION_NUMBER"

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

Tagged:

#### Issue · Github December 2015 by Sheila

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

• Cambridge, MA

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.

• 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

• Cambridge, MA

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?

• 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


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

#### Issue · Github December 2015 by Sheila

Issue Number
411
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
chandrans

@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

• Cambridge, MA

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.

• Hey @Sheila and and @Geraldine_VdAuwera
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 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

• thanks for the effort @Sheila very much appreciated!!