Hi,
I would say this is my fault but would you mind bring in sync your file in the hg38 bundle on your FTP server?
java -jar GATK/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar -T BaseRecalibrator --num_threads 16 -R ftp.broadinstitute.org/bundle/hg38/hg38bundle/Homo_sapiens_assembly38.fasta -I sample-PB.realignedtogether.bam --knownSites ftp.broadinstitute.org/bundle/hg38/hg38bundle/dbsnp_144.hg38.vcf --knownSites ussd-ftp.illumina.com/2016-1.0/hg38/small_variants/NA12877/NA12877.vcf --knownSites ussd-ftp.illumina.com/2016-1.0/hg38/small_variants/NA12878/NA12878.vcf -o sample-PB.recalibration_data.table.txt
INFO 14:51:31,644 HelpFormatter - -------------------------------------------------------------------------------------------
INFO 14:51:31,648 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29
INFO 14:51:31,648 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 14:51:31,648 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO 14:51:31,648 HelpFormatter - [Mon Aug 01 14:51:31 CEST 2016] Executing on Linux 2.6.32-573.12.1.el6.Bull.88.x86_64 amd64
INFO 14:51:31,648 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_102-b14 JdkDeflater
INFO 14:51:31,652 HelpFormatter - Program Args: -T BaseRecalibrator --num_threads 16 -R ftp.broadinstitute.org/bundle/hg38/hg38bundle/Homo_sapiens_assembly38.fasta -I sample-PB.realignedtogether.bam --knownSites ftp.broadinstitute.org/bundle/hg38/hg38bundle/dbsnp_144.hg38.vcf --knownSites ussd-ftp.illumina.com/2016-1.0/hg38/small_variants/NA12877/NA12877.vcf --knownSites ussd-ftp.illumina.com/2016-1.0/hg38/small_variants/NA12878/NA12878.vcf -o sample-PB.recalibration_data.table.txt
INFO 14:51:31,659 HelpFormatter - Executing as mmokrejs@login2 on Linux 2.6.32-573.12.1.el6.Bull.88.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_102-b14.
INFO 14:51:31,660 HelpFormatter - Date/Time: 2016/08/01 14:51:31
INFO 14:51:31,660 HelpFormatter - -------------------------------------------------------------------------------------------
INFO 14:51:31,660 HelpFormatter - -------------------------------------------------------------------------------------------
INFO 14:51:31,700 GenomeAnalysisEngine - Strictness is SILENT
INFO 14:51:33,324 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 14:51:33,331 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 14:51:33,456 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
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: Input files ftp.broadinstitute.org/bundle/hg38/hg38bundle/dbsnp_144.hg38.vcf and reference have incompatible contigs. Please see https://www.broadinstitute.org/gatk/guide/article?id=63for more information. Error details: No overlapping contigs found.
ERROR ftp.broadinstitute.org/bundle/hg38/hg38bundle/dbsnp_144.hg38.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT]
ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270713v1_random, chr1_KI270714v1_random, chr2_KI270715v1_random, chr2_KI270716v1_random, chr3_GL000221v1_random, chr4_GL000008v2_random, chr5_GL000208v1_random, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr11_KI270721v1_random, chr14_GL000009v2_random, chr14_GL000225v1_random, chr14_KI270722v1_random, chr14_GL000194v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr15_KI270727v1_random, ...
I thought I can use your files together without a change.
BTW: it would have been nice if the genomic reference was compressed using bgzip and not gzip.