BR: HMMRATAC throws an exception when using samblaster-deduped bam file even with --removeDuplicates false

[omegahh]

To Reproduce the bam file has been sorted by samtools sort and deduplicated by samblaster.

Screenshots

System (please complete the following information):

• OS: centos7
• JRE version: openJDK 8
• HMMRATAC Version: 1.2.10

[jitsedesmet]

Hi! I'm a computer major at Ghent university. We have a project that requires us to fix some bugs or help people solve them. Could you explain what happens right now and what you expect to happen? I would be glad to take a look at your problem, but I don't understand it 100%.