I am trying to remove PCR duplicate from my sam file. When I use samtools rmdup, it will abort in the middle.
samtools rmdup my_data.sam my_data_rmdup.sam [bam_rmdup_core] processing reference chr6... .... samtools(5713,0x7fffa2def340) malloc: *** error for object 0x7f999f600508: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6
I can't solve this issue. My condition is following ProductName: Mac OS X ProductVersion: 10.13.2 32G memory samtools Version: 1.6 (using htslib 1.6)
I would be happy if someone gave me an advice. Thank you.