Are you using the latest version of samtools and HTSlib? If not, please specify.
(run samtools --version)
1.10
Please describe your environment.
- OS Linux Centos and Ubuntu tested both OS
- machine architecture x86_64
- compiler gcc 9.2
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
samtools merge out.bam in1.bam in2.bam
Segmentation fault
This happens regardless of other options -O BAM --thread 6
If using bamtools merge no problem. If I convert the two input bam files into sam file, then samtools merge has no problems.
There must be something strange happened before this step.
I used bwamem2 mem did the alignment. That could be the reason. I have used samtools merge for a long time. only recently I see this. I will keep updating this bug. May compile the latest version to see, the bug is still there.
Are you using the latest version of samtools and HTSlib? If not, please specify.
(run
samtools --version)1.10
Please describe your environment.
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
samtools merge out.bam in1.bam in2.bam
Segmentation fault
This happens regardless of other options -O BAM --thread 6
If using bamtools merge no problem. If I convert the two input bam files into sam file, then samtools merge has no problems.
There must be something strange happened before this step.
I used bwamem2 mem did the alignment. That could be the reason. I have used samtools merge for a long time. only recently I see this. I will keep updating this bug. May compile the latest version to see, the bug is still there.