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