Hi GATK Teams,

I tried to run GatherVcfs ( version 4.1.8.1 ) to gather all chromosome phased vcf files of which heads were recoded but got error "There was a problem with gathering the INPUT.java.lang.NullPointerException".

My script is as following:

gatk=/PATH/gatk
time $gatk --java-options "-Xmx1G" GatherVcfs \
-I JC.chr1.filter.vcf.gz \
-I JC.chr2.filter.vcf.gz \
-I JC.chr3.filter.vcf.gz \
-I JC.chr4.filter.vcf.gz \
-I JC.chr5.filter.vcf.gz \
-I JC.chr6.filter.vcf.gz \
-I JC.chr7.filter.vcf.gz \
-I JC.chr8.filter.vcf.gz \
-I JC.chr9.filter.vcf.gz \
-I JC.chr10.filter.vcf.gz \
-I JC.chr11.filter.vcf.gz \
-I JC.chr12.filter.vcf.gz \
-I JC.chr13.filter.vcf.gz \
-I JC.chr14.filter.vcf.gz \
-I JC.chr15.filter.vcf.gz \
-I JC.chr16.filter.vcf.gz \
-I JC.chr17.filter.vcf.gz \
-I JC.chr18.filter.vcf.gz \
-I JC.chr19.filter.vcf.gz \
-I JC.chr20.filter.vcf.gz \
-I JC.chr21.filter.vcf.gz \
-I JC.chr22.filter.vcf.gz \
--CREATE_INDEX false \
-O SW709.filter.phased.vcf.gz

And the following is the running log:

12:57:20.481 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/PATH/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Sat Aug 22 12:57:20 CST 2020] GatherVcfs --INPUT JC.chr1.filter.vcf.gz --INPUT JC.chr2.filter.vcf.gz --INPUT JC.chr3.filter.vcf.gz --INPUT JC.chr4.filter.vcf.gz --INPUT JC.chr5.filter.vcf.gz --INPUT JC.chr6.filter.vcf.gz --INPUT JC.chr7.filter.vcf.gz --INPUT JC.chr8.filter.vcf.gz --INPUT JC.chr9.filter.vcf.gz --INPUT JC.chr10.filter.vcf.gz --INPUT JC.chr11.filter.vcf.gz --INPUT JC.chr12.filter.vcf.gz --INPUT JC.chr13.filter.vcf.gz --INPUT JC.chr14.filter.vcf.gz --INPUT JC.chr15.filter.vcf.gz --INPUT JC.chr16.filter.vcf.gz --INPUT JC.chr17.filter.vcf.gz --INPUT JC.chr18.filter.vcf.gz --INPUT JC.chr19.filter.vcf.gz --INPUT JC.chr20.filter.vcf.gz --INPUT JC.chr21.filter.vcf.gz --INPUT JC.chr22.filter.vcf.gz --OUTPUT SW709.filter.phased.vcf.gz --CREATE_INDEX false --REORDER_INPUT_BY_FIRST_VARIANT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
Aug 22, 2020 12:57:21 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Sat Aug 22 12:57:21 CST 2020] Executing as qianxiaobo@cngb-compute-m16-7.cngb.sz.hpc on Linux 2.6.32-696.30.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.8.1
INFO 2020-08-22 12:57:21 GatherVcfs Checking inputs.
INFO 2020-08-22 12:57:22 GatherVcfs Checking file headers and first records to ensure compatibility.
ERROR 2020-08-22 12:57:22 GatherVcfs There was a problem with gathering the INPUT.java.lang.NullPointerException
[Sat Aug 22 12:57:22 CST 2020] picard.vcf.GatherVcfs done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=643301376
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Using GATK jar /PATH/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx1G -jar /PATH/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar GatherVcfs -I JC.chr1.filter.vcf.gz -I JC.chr2.filter.vcf.gz -I JC.chr3.filter.vcf.gz -I JC.chr4.filter.vcf.gz -I JC.chr5.filter.vcf.gz -I JC.chr6.filter.vcf.gz -I JC.chr7.filter.vcf.gz -I JC.chr8.filter.vcf.gz -I JC.chr9.filter.vcf.gz -I JC.chr10.filter.vcf.gz -I JC.chr11.filter.vcf.gz -I JC.chr12.filter.vcf.gz -I JC.chr13.filter.vcf.gz -I JC.chr14.filter.vcf.gz -I JC.chr15.filter.vcf.gz -I JC.chr16.filter.vcf.gz -I JC.chr17.filter.vcf.gz -I JC.chr18.filter.vcf.gz -I JC.chr19.filter.vcf.gz -I JC.chr20.filter.vcf.gz -I JC.chr21.filter.vcf.gz -I JC.chr22.filter.vcf.gz --CREATE_INDEX false -O SW709.filter.phased.vcf.gz

There is no other ERROR information in this log file so that I do not know how to solve it.

Please note that I rehead the chromosome vcf file like this:

##fileformat=VCFv4.2
##filedate=20200624
##source="beagle.13Mar20.38e.jar"
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated ALT Allele Frequencies">
##INFO=<ID=DR2,Number=1,Type=Float,Description="Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose">
##INFO=<ID=IMP,Number=0,Type=Flag,Description="Imputed marker">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=A,Type=Float,Description="estimated ALT dose [P(RA) + 2*P(AA)]">

I am not sure this issue will impact on GatherVcfs or not.

 Hope for your reply.