To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

DepthOfCoverage error

gibberwockygibberwocky UKMember
edited November 2014 in Ask the GATK team

I'm getting the following error in GATK 3.2-2:

MESSAGE: SAM/BAM file /home/dwragg/work/Analysis/TEST/AOC35_ATCACG_L008/AOC35_ATCACG_L008_bootstrap.bam is malformed: Program record with group id GATK PrintReads already exists in SAMFileHeader!

When attempting to calclate depth of coverage:

java -d64 -jar ${GATK}/GenomeAnalysisTK.jar \ -T DepthOfCoverage \ -R ${REF} \ -I ${OUT}/${SAMPLE}/${SAMPLE}_bootstrap.bam \ -o ${OUT}/${SAMPLE}/metrics/${SAMPLE}_GATKcov \ -ct 2 -ct 5 -ct 8 \ --omitDepthOutputAtEachBase \ --omitIntervalStatistics \ --omitLocusTable \ -l FATAL

I'm assuming this is not normal as everything was working fine in 3.1-1. Ironically I recently switched to 3.2-2 because the RealignerTargetCreator was giving me an Unsupported major.minor version 51.0 error. I'm running Java 1.7.0-b147.


I've since noticed that the BAM file was created with GATK version 2.4-9-g532efad. So the 'current' and 'latest' software filing system in place here appears to have failed. I can confirm that GATK v3.2-2 DepthOfCoverage tool generates the above program record group id error. I'll chase the administrators down to ensure the latest GATK version is installed and start from scratch.

Post edited by gibberwocky on


Sign In or Register to comment.