GATK Best Practices HaplotypeCaller Multi-sample Error

Question

[vctrm67]

I am running the HaplotypeCaller as a part of the GATK pipeline on a single BAM file. I keep getting the error:

A USER ERROR has occurred: Argument --emitRefConfidence has a bad value: Can only be used in single sample mode currently. 
Use the sample_name argument to run on a single sample out of a multi-sample BAM file.

However, I am fairly confident that there is only one sample in the BAM file. I tried neglecting the -ERC GVCF as per some suggestions (haplotypecaller can not run in single bam file) but get this message instead:

htsjdk.samtools.util.RuntimeIOException: Unable to close index for file: ... 
...
Caused by: java.io.IOException: Terminator block not found after closing BGZF file: ...

However, as some people suggested (https://gatkforums.broadinstitute.org/gatk/discussion/11202/haplotypecaller-error-in-the-middle-of-processing), I increased the memory to over 100G and it didn't solve the problem.

Does anyone have any suggestions?

Answer 1

[Pierre Lindenbaum]

what is the exact command line ?

Show us the read-group of the bam (samtools view -H in.bam | grep -F '@RG' )

[vctrm67]

@RG ID:DS-bkm-085-N_AACTCACC_L001_R_001_RG  SM:DS-bkm-085-N_AACTCACC_L001_R_001 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L001_R_002_RG  SM:DS-bkm-085-N_AACTCACC_L001_R_002 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L002_R_001_RG  SM:DS-bkm-085-N_AACTCACC_L002_R_001 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L002_R_002_RG  SM:DS-bkm-085-N_AACTCACC_L002_R_002 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L003_R_001_RG  SM:DS-bkm-085-N_AACTCACC_L003_R_001 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L003_R_002_RG  SM:DS-bkm-085-N_AACTCACC_L003_R_002 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L004_R_001_RG  SM:DS-bkm-085-N_AACTCACC_L004_R_001 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L004_R_002_RG  SM:DS-bkm-085-N_AACTCACC_L004_R_002 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L005_R_001_RG  SM:DS-bkm-085-N_AACTCACC_L005_R_001 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L005_R_002_RG  SM:DS-bkm-085-N_AACTCACC_L005_R_002 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L007_R_001_RG  SM:DS-bkm-085-N_AACTCACC_L007_R_001 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_AACTCACC_L007_R_002_RG  SM:DS-bkm-085-N_AACTCACC_L007_R_002 LB:lib_name PL:illumina

[Dave Carlson]

In the above, you can see that you have multiple sample names (text following "SM:"), thus GATK is treating this as a multi-sample BAM file.

[Pierre Lindenbaum]

your bam contains more than one sample (SM:...)

[vctrm67]

In that case, do you know how to resolve the error regarding

htsjdk.samtools.util.RuntimeIOException: Unable to close index for file: ... 
...
Caused by: java.io.IOException: Terminator block not found after closing BGZF file: ...

[Pierre Lindenbaum]

you have to change the header of your bam to change those multiple @SM into one. For example use: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.0.0/picard_sam_AddOrReplaceReadGroups.php

In that case, do you know how to resolve the error regarding

if samtools view your.bam fails too, it means that your bam is corrupted and you 'll have to re-generateit.

[chenqing]

Have you solved your problem? I have the same question with you,but I can't solve it using website: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.0.0/picard_sam_AddOrReplaceReadGroups.php