I am using the
samtools view -b -S -o command and I seem to get a new error every time I run the command.
I will get
[sam_read1] reference 'AMELIA:269' is recognized as '*'.
[main_samview] truncated file.
Parse error at line 5177839: sequence and quality are inconsistent
Aborted (core dumped) this line changes everytime
[sam_read1] reference 'AMELIA:269:C1EUFACXX:2:1101:12' is recognized as '*'.
[main_samview] truncated file.'
The sam input file was created with the bwa