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Full Discussion: Redirecting STDERR to file and screen, STDOUT only to file
Top Forums Shell Programming and Scripting Redirecting STDERR to file and screen, STDOUT only to file Post 302697711 by alister on Friday 7th of September 2012 09:06:58 AM
Old 09-07-2012
The y-shaped hose and bucket analogy paints a memorable image. Nicely done. The only thing I'd add, explicitly (it's implied in your explanation), is that pipe redirection occurs before other, left-to-right redirections.

Quote:
Originally Posted by bakunin
The only uncertainty left is that i am not sure if the exact sequence of the messages will be preserved...
Even without the pipe and redirections, you can't depend on your average script/executable to emit messages in the exact order that they're generated, since typically a mix of unbuffered (stderr) and buffered (stdout) streams are used.

Of much greater importance is that script 2>&1 1>/some/file | tee -a /some/file involves multiple processes writing to the same file without any form of communication. Writes from script will clobber writes from tee, or vice versa. If they at least shared a file descriptor, while one message could still split another in two, there would never be any overwriting.

Regards,
Alister
Last edited by alister; 09-07-2012 at 10:47 AM..
This User Gave Thanks to alister For This Post:
bakunin
 

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LEARN ABOUT DEBIAN

fastq_quality_trimmer

FASTQ_QUALITY_TRIMMER(1)					   User Commands					  FASTQ_QUALITY_TRIMMER(1)

NAME

       fastq_quality_trimmer - Filters sequences based on quality

DESCRIPTION

       usage:  fastq_quality_trimmer  [-h]  [-v]  [-t  N]  [-l	N] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.1 by A. Gordon (gor-
       don@cshl.edu)

       [-h]   = This helpful help screen.

       [-t N] = Quality threshold - nucleotides with lower

	      quality will be trimmed (from the end of the sequence).

       [-l N] = Minimum length - sequences shorter than this (after trimming)

	      will be discarded. Default = 0 = no minimum length.

       [-z]   = Compress output with GZIP.

       [-i INFILE]
	      = FASTQ input file. default is STDIN.

	      [-o OUTFILE] = FASTQ output file. default is STDOUT.  [-v]	 = Verbose - report number of sequences.

       If [-o] is specified,
	      report will be printed to STDOUT.

	      If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR.

SEE ALSO

       The quality of this automatically generated manpage might be insufficient.  It is suggested to visit

	      http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

       to get a better layout as well as an overview about connected FASTX tools.

fastq_quality_trimmer 0.0.13.1					    April 2012						  FASTQ_QUALITY_TRIMMER(1)
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