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Running fastp in quiet mode. #563

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otradnaya opened this issue May 26, 2024 · 2 comments
Open

Running fastp in quiet mode. #563

otradnaya opened this issue May 26, 2024 · 2 comments

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@otradnaya
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otradnaya commented May 26, 2024

Hi, it appears fastp writes progress notes to stderr. Is it possible to suppress stderr output except errors and warnings? I.e., nothing would be written to stderr unless fastp fails. Thanks!

@otradnaya otradnaya changed the title Run fastp in quiet mode . May 26, 2024
@otradnaya otradnaya changed the title . Running fastp in quiet mode. May 26, 2024
@sfchen
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sfchen commented Jul 3, 2024

suggest to use pipes

@otradnaya
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Sorry, please let me clarify. Here are three sample lines from your code:
cerr << "reads passed filter: " << mFilterReadStats[PASS_FILTER] << endl.
cerr << "ERROR: file '" << s << "' doesn't exist, quit now" << endl;
cerr << "WARNING: the algorithm is wrong! uncorrected + corrected ...

In a future release, would it make sense to redirect informational messages like the first line to cout instead of cerr? Errors and warnings can continue to be printed to cerr.

What do you think? Thanks!

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