why do the header of bwa mapping sam files show [M::main_mem]

Question

[szp770]

why does the header of my bwa mapping file showing: """ [M::main_mem] read 1198380 sequences (100000017 bp)... """ I cannot do any further analysis using this file.

Answer 1

[Pierre Lindenbaum]

My guess is in your workflow you're both redirecting stderr and stdout to the the same file. ( Are you using nohup for example ?)

[M::main_mem] read 1198380 sequences (100000017 bp)... """

is a message that is displayed on stderr: https://github.com/lh3/bwa/blob/f1d1fd7c42e16f6006da77bf81e402eb531dbac2/fastmap.c#L85

[szp770]

Yes, I used nohup. It is solved if I run the command in a *.sh file.