REQUIRED for all errors and issues:
a) GATK version used:

module load GATK/3.6.0 
b) Exact command used:

GenomeAnalysisTK -nt 8 -T GenotypeGVCFs \
-R persian_walnut_junglans_regia_chrs_sept18.fasta \
--variant SRR11497836.vcf.gz \

...............
 
c) Entire program log:This software stack is maintained by the Purdue Bioinformatics Core. Please
direct inquiries regarding Bioinformatics software to bioinformatics@purdue.edu
INFO  06:32:27,844 HelpFormatter - ----------------------------------------------------------------------------------
INFO  06:32:27,846 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29
INFO  06:32:27,846 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO  06:32:27,847 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO  06:32:27,847 HelpFormatter - [Thu Mar 10 06:32:27 EST 2022] Executing on Linux 3.10.0-1062.9.1.el7.x86_64 amd64
INFO  06:32:27,847 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_242-b08 JdkDeflater
INFO  06:32:27,849 HelpFormatter - Program Args: -nt 8 -T GenotypeGVCFs -R persian_walnut_junglans_regia_chrs_sept18.fasta --variant SRR11497836.vcf.gz --variant SRR11497835.vcf.gz --variant SRR11497834.vcf.gz --variant SRR11497833.vcf.gz --variant SRR11497832.vcf.gz --variant SRR11497831.vcf.gz --variant SRR11497830.vcf.gz --variant SRR11497829.vcf.gz --variant SRR11497828.vcf.gz --variant SRR11497827.vcf.gz --variant SRR11497826.vcf.gz --variant SRR11497825.vcf.gz --variant SRR11497824.vcf.gz --variant SRR11497823.vcf.gz --variant SRR11497822.vcf.gz --variant SRR11497821.vcf.gz --variant SRR11497820.vcf.gz --variant SRR11497819.vcf.gz --variant SRR11497818.vcf.gz --variant SRR11497817.vcf.gz --variant SRR11497816.vcf.gz --variant SRR11497815.vcf.gz --variant SRR11497814.vcf.gz --variant SRR11497813.vcf.gz --variant SRR11497812.vcf.gz --variant SRR11497811.vcf.gz --variant SRR11497810.vcf.gz --variant SRR11497809.vcf.gz --variant SRR11497808.vcf.gz --variant SRR11497807.vcf.gz --variant SRR11497806.vcf.gz --variant SRR11497805.vcf.gz --variant SRR11497804.vcf.gz --variant SRR11497803.vcf.gz --variant SRR11497802.vcf.gz --variant SRR11497800.vcf.gz --variant SRR11497799.vcf.gz --variant SRR11497798.vcf.gz --variant SRR11497797.vcf.gz --variant SRR11497796.vcf.gz --variant SRR11497795.vcf.gz --variant SRR11497794.vcf.gz --variant SRR11497793.vcf.gz --variant SRR11497792.vcf.gz --variant SRR11497790.vcf.gz --variant SRR11497791.vcf.gz --variant SRR11497789.vcf.gz --variant SRR11497788.vcf.gz --variant SRR11497787.vcf.gz --variant SRR11497786.vcf.gz --variant SRR11497785.vcf.gz --variant SRR11497783.vcf.gz --variant SRR11497784.vcf.gz --variant SRR11497782.vcf.gz --variant SRR11497781.vcf.gz --variant SRR11497780.vcf.gz --variant SRR11497779.vcf.gz --variant SRR11497778.vcf.gz --variant SRR11497777.vcf.gz --variant SRR11497776.vcf.gz --variant SRR11497775.vcf.gz --variant SRR11497774.vcf.gz --variant SRR11497773.vcf.gz --variant SRR11497772.vcf.gz --variant SRR8772786.vcf.gz --variant SRR6804856.vcf.gz --variant SRR6804855.vcf.gz --variant SRR6804854.vcf.gz --variant SRR6804853.vcf.gz --variant SRR6804852.vcf.gz --variant SRR6804851.vcf.gz --variant SRR6804850.vcf.gz --variant SRR6804849.vcf.gz --variant SRR6804848.vcf.gz --variant SRR6804847.vcf.gz --variant SRR6804846.vcf.gz --variant SRR6804845.vcf.gz --variant SRR6804843.vcf.gz --variant SRR6804842.vcf.gz --variant SRR6804841.vcf.gz --variant SRR6804840.vcf.gz --variant SRR6793981.vcf.gz --variant SRR6793980.vcf.gz --variant SRR6793979.vcf.gz --variant SRR6793978.vcf.gz --variant SRR6793977.vcf.gz --variant SRR6793976.vcf.gz --variant SRR6793975.vcf.gz --variant SRR6793974.vcf.gz --variant SRR6793973.vcf.gz --variant SRR6793972.vcf.gz --variant SRR6793971.vcf.gz --variant SRR6793970.vcf.gz --variant SRR6793969.vcf.gz --variant SRR6793968.vcf.gz --variant SRR6793967.vcf.gz --variant SRR6793966.vcf.gz --variant SRR6793965.vcf.gz --variant SRR14085898.vcf.gz --variant SRR13361464.vcf.gz --variant SRR13361463.vcf.gz --variant Cmy_IYBZ.vcf.gz --variant Cmy_IXLR.vcf.gz --variant Cmy_IXLQ.vcf.gz --variant Cilli.vcf.gz --variant Ccord_IXSD.vcf.gz --variant Ccord_IXIH.vcf.gz --variant Caqu.vcf -o all_carya_wg.vcf.gz
INFO  06:32:27,855 HelpFormatter - Executing as aebrahi@brown-a444.rcac.purdue.edu on Linux 3.10.0-1062.9.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_242-b08.
INFO  06:32:27,855 HelpFormatter - Date/Time: 2022/03/10 06:32:27
INFO  06:32:27,855 HelpFormatter - ----------------------------------------------------------------------------------
INFO  06:32:27,855 HelpFormatter - ----------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.6-0-g89b7209):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Could not read file /scratch/brown/aebrahi/regia_ref2/carya/WG/SRR11497836.vcf.gz because file 'SRR11497836.vcf.gz' does not exist
##### ERROR ------------------------------------------------------------------------------------------
(END)
 

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