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Full Discussion: Attach filename to wc results on massive number of files
Top Forums Shell Programming and Scripting Attach filename to wc results on massive number of files Post 303032349 by yifangt on Friday 15th of March 2019 12:46:01 PM
Old 03-15-2019
parallel to restrict the process number
@bakunin @all
Your comments are exactly what I wanted to catch. Here, I reformed my script with GNU parallel to control the process limits, but I hit another wall:
Code:
parallel -a $LIST1 -j 48 "(printf "%s\t%s\n" {} $(zcat {}_R1.fq.gz | wc -l)) >> raw_reads_count.table1"
------------------------------------------------------
a 0 >> raw_reads_count.table1
bb 0 >> raw_reads_count.table1
ccc 0 >> raw_reads_count.table1
xyz 0 >> raw_reads_count.table1

The problem seems with the parallel placeholder expansion. Is it because of the too many layers of parenthesis () ? Need to get myself familiar with quoting in bash.
Thanks for any help!
======================================================================================
It seems to me this is the final solution:

Code:
parallel -a $LIST1 -j 48 "(echo -n {}' '; (zcat ${RAW_DIR1}/{}_R1.fq.gz | wc -l)) > {}_counts.tmp"
cat *_counts.tmp >> raw_reads_count.table1

Thanks you all for the help!
Last edited by yifangt; 03-15-2019 at 03:36 PM..
 

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LEARN ABOUT DEBIAN

colorgccrc

COLORGCCRC(5)							File Formats Manual						     COLORGCCRC(5)

NAME

       colorgccrc - configuration file for colorgcc

DESCRIPTION

       A colorgccrc configuration file is used to configure the highlighting of the compiler output from colorgcc.

SYNTAX

       Each  line  consists  of  a  keyword  designating  a configuration variable.  The keyword is followed by `:' and then one or several values
       (depending on the keyword).  Lines beginning with a hash mark `#' are comments.

CONFIGURATION VARIABLES

       g++ | gcc | c++ | cc | g77 | gcj | gnat | gpc
	      Specifies the paths to the compilers.  Takes one value; a path to the compiler.

       nocolor
	      Specifies what terminal types colorization should be disabled on.  Takes one or several values, separated by whitespace.

       srcColor
	      Specifies the highlighting attributes source-code should be given.  Takes one or several color attributes.  See  the  section  COLOR
	      ATTRIBUTES for more information.

       introColor
	      Specifies  the  highlighting  attributes	for normal compiler output.  Takes one or several color attributes.  See the section COLOR
	      ATTRIBUTES for more information.

       warningFileNameColor | errorFileNameColor
	      Specifies the highlighting attributes for the filename in a  warning  or	an  error,  respectively.   Takes  one	or  several  color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

       warningNumberColor | errorNumberColor
	      Specifies  the  highlighting  attributes	for  the  line-number  in a warning or an error, respectively.	Takes one or several color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

       warningMessageColor | errorMessageColor
	      Specifies the highlighting attributes for the message-text in a warning or an error,  respectively.   Takes  one	or  several  color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

COLOR ATTRIBUTES

       The following attributes are valid for highlighting.

       clear, reset

       bold, underline, underscore, blink, reverse, concealed

       black, red, green, yellow, blue, magenta, cyan, white

       on_black, on_red, on_green, on_yellow, on_blue, on_magenta, on_cyan, on_white

SEE ALSO

       gcc(1), colorgcc(1)

HISTORY

       Jan 15 2003: Initial version of this manual-page.

REPORTING BUGS

       Report bugs to <jmoyers@geeks.com>

AUTHORS

       Jamie Moyers <jmoyers@geeks.com> is the author of colorgcc.

       This  manual  page  was	written  by Joe Wreschnig <piman@sacredchao.net>, and modified by David Weinehall <tao@debian.org>, for the Debian
       GNU/Linux system (but may be used by others).

COPYRIGHT

       Copyright (C) 2003 Jamie Moyers
       This is free software; see the source for copying conditions.  There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU-
       LAR PURPOSE.

								   Jan 15, 2003 						     COLORGCCRC(5)
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