Hello all,
I'm trying to run HaplotypeCaller on a bam that I've created following the Best Practices, however it fails and gives me the following error message:
ERROR ------------------------------------------------------------------------------------------
That is literally the extent of the message. Preceding that is a list of scaffold/contig titles ending with a ']', proceedign that is my terminal command line.
I turned on logging (added "-log log.txt" to the end of my command) and the log contained the following:
INFO 11:30:11,884 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:30:11,886 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29
INFO 11:30:11,886 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 11:30:11,886 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO 11:30:11,886 HelpFormatter - [Fri Sep 02 11:30:11 EDT 2016] Executing on Linux 3.16.0-77-generic amd64
INFO 11:30:11,886 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13 JdkDeflater
INFO 11:30:11,889 HelpFormatter - Program Args: -T HaplotypeCaller -R Csativa_genome.fa -I GBS_Csativa_clean_dedup.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o GBS_Csativa_clean_raw-variants.vcf -log HC_clean.log
INFO 11:30:11,891 HelpFormatter - Executing as root@Banting on Linux 3.16.0-77-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13.
INFO 11:30:11,891 HelpFormatter - Date/Time: 2016/09/02 11:30:11
INFO 11:30:11,892 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:30:11,892 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:30:11,905 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:55:56,387 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
INFO 11:55:56,392 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:55:58,019 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 1.63
INFO 11:55:59,327 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
The command I'm using is:
java -jar /Apps/gatk/GenomeAnalysisTK.jar -T HaplotypeCaller -R Csativa_genome.fa -I GBS_Csativa_clean_dedup.bam --genotyping_mode DISCOVERY -hets 0.01 -stand_emit_conf 10 -stand_call_conf 30 -o GBS_Csativa_clean_raw-variants.vcf
Any assistance would be appreciated, even if only to identify what the error actually is, I couldn't find anything on the forums with this kind of non-specific error. If you need more information I will gladly post it
