GATK4.1.1.0---HaplotypeCaller :HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output

Question

[nw_hyz]

Hi everyone, I meet a difficult problem...

java -Xmx40g -jar /data1/user/software/gatk-4.1.1.0/gatk-package-4.1.1.0-local.jar HaplotypeCaller -R genomic.fna -I x11fq/x11.sort.mkdup.bam -O x11fq/x11.g.vcf

12:33:15.225 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data1/user/wangyl/software/gatk-4.1.1.0/gatk-package-4.1.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Apr 10, 2019 12:33:17 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
12:33:17.302 INFO  HaplotypeCaller - ------------------------------------------------------------
12:33:17.303 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.1.0
12:33:17.303 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
12:33:27.677 INFO  HaplotypeCaller - Initializing engine
12:33:28.076 INFO  HaplotypeCaller - Done initializing engine
**12:33:28.096 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
12:33:28.103 INFO  HaplotypeCaller - Shutting down engine**
[April 10, 2019 12:33:28 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.21 minutes.
Runtime.totalMemory()=1401421824
**java.lang.IllegalArgumentException: samples cannot be empty**
    at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:724)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel.<init>(ReferenceConfidenceModel.java:116)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.initialize(HaplotypeCallerEngine.java:205)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.<init>(HaplotypeCallerEngine.java:157)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.onTraversalStart(HaplotypeCaller.java:224)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:982)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
    at org.broadinstitute.hellbender.Main.main(Main.java:291)

I can't deal with it. someone can help me? Thanks a lot.

[finswimmer]

Hello and welcome to biostars nw_hyz ,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[nw_hyz]

Wow,Thank you!

I found this mistake after publish it... and I don't know how to delete this post...embarrased.
I will try to learn

Thank you!

Answer 1

[Pierre Lindenbaum]

the error is here: **java.lang.IllegalArgumentException: samples cannot be empty**

I suspect there is no Read group in x11fq/x11.sort.mkdup.bam or the @RG/SM field is empty.

[nw_hyz]

Thank you!
I thought it isn't important,so skip this step of add @RG, TOO naive,HAHA.

I will add it and try again.
Thank you very much!(there is no emoticon, sad)

[Pierre Lindenbaum]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[nw_hyz]

Yeah, I ignore the " √ ", just cilck the thumb, Thanks about your patience and enthusiasm.

and...Should I consult you for one question? How to modify that code. I find you helped me just now.

Thanks!

Answer 2

[luosuxingfuzhilu]

add @RG annotation by following command:

java -jar picard.jar AddOrReplaceReadGroups \
I=input.bam \
O=output.bam \
RGLB=lib1 \
RGPL=illumina \
RGPU=unit1 \
RGSM=ILoveYou