Hi,
it seems GATK does not relaize that it has opened a vcf.gz (actually vcf.bgz file).
java -Djavaio.tmpdir=. -jar /scratch/mmokrejs/GATK/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /scratch/mmokrejs/db/ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/GRCh37.p13.genome.GRC-style.minimal.fasta -I 5584.removed_duplicates.bam -known /scratch/mmokrejs/db/ftp.broadinstitute.org/bundle/2.8/b37/1000G_phase3_v4_20130502.sites.vcf.gz -known /scratch/mmokrejs/db/ftp.broadinstitute.org/bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz -known /scratch/mmokrejs/db/ftp.broadinstitute.org/bundle/2.8/b37/hapmap_3.3.b37.vcf.gz -known /scratch/mmokrejs/db/ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/GATK/common_all_20160601.sorted.vcf.gz -known /scratch/mmokrejs/db/ussd-ftp.illumina.com/2016-1.0/hg19/small_variants/NA12877/NA12877.vcf.gz -known /scratch/mmokrejs/db/ussd-ftp.illumina.com/2016-1.0/hg19/small_variants/NA12878/NA12878.vcf.gz -o 5584.forIndelRealigner.intervals INFO 16:51:39,199 HelpFormatter - ------------------------------------------------------------------------------------------ INFO 16:51:39,202 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18 INFO 16:51:39,202 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute INFO 16:51:39,202 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk INFO 16:51:39,202 HelpFormatter - [Sat Jan 21 16:51:39 CET 2017] Executing on Linux 2.6.32-642.6.2.el6.Bull.104.x86_64 amd64 INFO 16:51:39,202 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_112-b15 INFO 16:51:39,206 HelpFormatter - Program Args: -T RealignerTargetCreator -R /scratch/mmokrejs/db/ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/GRCh37.p13.genome.GRC-style.minimal.fasta -I 5584.removed_duplicates.bam -known /scratch/mmokrejs/db/ftp.broadinstitute.org/bundle/2.8/b37/1000G_phase3_v4_20130502.sites.vcf.gz -known /scratch/mmokrejs/db/ftp.broadinstitute.org/bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz -known /scratch/mmokrejs/db/ftp.broadinstitute.org/bundle/2.8/b37/hapmap_3.3.b37.vcf.gz -known /scratch/mmokrejs/db/ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/GATK/common_all_20160601.sorted.vcf.gz -known /scratch/mmokrejs/db/ussd-ftp.illumina.com/2016-1.0/hg19/small_variants/NA12877/NA12877.vcf.gz -known /scratch/mmokrejs/db/ussd-ftp.illumina.com/2016-1.0/hg19/small_variants/NA12878/NA12878.vcf.gz -o 5584.forIndelRealigner.intervals INFO 16:51:39,211 HelpFormatter - Executing as mmokrejs@login1 on Linux 2.6.32-642.6.2.el6.Bull.104.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_112-b15. INFO 16:51:39,211 HelpFormatter - Date/Time: 2017/01/21 16:51:39 INFO 16:51:39,211 HelpFormatter - ------------------------------------------------------------------------------------------ INFO 16:51:39,211 HelpFormatter - ------------------------------------------------------------------------------------------ INFO 16:51:39,257 GenomeAnalysisEngine - Strictness is SILENT INFO 16:51:39,366 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 16:51:39,374 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 16:51:39,406 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03 WARN 16:51:39,803 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation WARN 16:51:39,804 IndexDictionaryUtils - Track known2 doesn't have a sequence dictionary built in, skipping dictionary validation WARN 16:51:39,804 IndexDictionaryUtils - Track known3 doesn't have a sequence dictionary built in, skipping dictionary validation WARN 16:51:39,804 IndexDictionaryUtils - Track known4 doesn't have a sequence dictionary built in, skipping dictionary validation WARN 16:51:39,804 IndexDictionaryUtils - Track known5 doesn't have a sequence dictionary built in, skipping dictionary validation WARN 16:51:39,804 IndexDictionaryUtils - Track known6 doesn't have a sequence dictionary built in, skipping dictionary validation INFO 16:51:39,950 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 16:51:40,233 GenomeAnalysisEngine - Done preparing for traversal INFO 16:51:40,234 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 16:51:40,234 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 16:51:40,234 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67): ##### 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://software.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: Line 128: there aren't enough columns for line ?BCp9?}ksc???g?W ???B??11? (we expected 9 tokens, and saw 1 ), for input source: /scratch/mmokrejs/db/ftp.broadinstitute.org/bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz
