The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
GATK HaplotypeCaller produces no output
Hi, A colleague was experiencing a very long run-time for a GATK HaplotypeCaller run and asked me to look at it. I noticed that although it had been running for about 5 days, it hadn't even created a vcf file and showed no progress on the stderr. The last line after 5 days of runtime was:
INFO 13:00:27,433 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
I extracted one of the scaffolds from the assembly (fasta and bam), created indexes for them and tested GATK on the minimal dataset and I could also replicate the problem, i.e. no progress and no output . I've attached the bam, fasta, indexes and command line and was wondering if you could identify why GATK seems to stall before analysing the bam file. The bam file is only a few MB, so I'd expect GATK to only take a few minutes to create output, but this is obviously not the case.