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Thank you for your patience!
BaseRecalibrator Hangs Without Error Message
I am using the BaseRecalibrator on a set of 20 samples that have been exome capture sequenced (~35x mapped coverage over 60Mb), and I am getting strange behavior. The BaseRecalibrator hangs after printing the message "Done initializing BAM readers." I've let it go for 16 hours, and nothing has changed. I've tried both single sample and merged BAM files with read groups, and the behavior is the same.
The command I am running is as follows
java -jar GenomeAnalysisTK.jar\ -T BaseRecalibrator\ -R reference.fasta\ --knownSites known_snps.vcf\ -I alignment.bam\ --covariate ContextCovariate\ --covariate CycleCovariate\ --covariate QualityScoreCovariate\ --covariate ReadGroupCovariate\ -o recalibration.table\ -nct 8
I am using the Java SE runtime version 1.8.0_45 and GATK version 3.5-0-g36282e4 on a 64-bit Linux server.
Is this a matter of just waiting longer, or is there likely to be some problem with my input files? Thank you!