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Full Discussion: Problem with process substitution
Top Forums Shell Programming and Scripting Problem with process substitution Post 302819265 by dietmar13 on Monday 10th of June 2013 01:50:29 PM
Old 06-10-2013
Problem with process substitution
i have tried process substitution, but run in some problems.

this works:
Code:
 
samtools view -h $SAMdir/$b.bam | htseq-count -m union -s no -q -t exon -i gene_id - $gtf > $b.count &

but this not:
Code:
 
htseq-count -m union -s no -q -t exon -i gene_id <(samtools view -h $SAMdir/$b.bam) $gtf > $b.count &

the error is not fundamental, and some (few) of the runs worked (i looped over a bunch of files). the error indicated a truncated sam-file, that means that one line of the file (which is in a specific format, the sam format) was malformed (some columns are missing). how can the above commands be different?
or has it to do with the multiple processes i started (using &)?
 

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set_color

set_color(1)							       fish							      set_color(1)

NAME

       set_color - set_color - set the terminal color

set_color - set the terminal color
   Synopsis
       set_color [-v --version] [-h --help] [-b --background COLOR] [COLOR]

   Description
       Change the foreground and/or background color of the terminal. COLOR is one of black, red, green, brown, yellow, blue, magenta, purple,
       cyan, white and normal.

       o -b, --background Set the background color

       o -c, --print-colors Prints a list of all valid color names

       o -h, --help Display help message and exit

       o -o, --bold Set bold or extra bright mode

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       o -v, --version Display version and exit

       Calling set_color normal will set the terminal color to whatever is the default color of the terminal.

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       set_color uses the terminfo database to look up how to change terminal colors on whatever terminal is in use. Some systems have old and
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       ncurses and recompile fish against it in order to fix this issue.

Version 1.23.1							  Sun Jan 8 2012						      set_color(1)
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