why do the header of bwa mapping sam files show [M::main_mem]
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6 months ago
szp770 ▴ 10

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.

shell bwa genome chip mapping • 303 views
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6 months ago

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

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

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