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Full Discussion: Badly placed ()'s
Top Forums Shell Programming and Scripting Badly placed ()'s Post 303006043 by drl on Thursday 26th of October 2017 09:10:03 AM
Old 10-26-2017
Hi.

Just a guess, change from:
Code:
fastqc -f fastq -o /data4/user/test/fastqc/ $i

to (by adding quotes):
Code:
fastqc -f fastq -o /data4/user/test/fastqc/ "$i"

Good luck ... cheers, drl
 

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SCRIPT(1)						    BSD General Commands Manual 						 SCRIPT(1)

NAME
script -- make typescript of terminal session SYNOPSIS
script [-adfpqr] [-c command] [file] DESCRIPTION
script makes a typescript of everything printed on your terminal. It is useful for students who need a hardcopy record of an interactive session as proof of an assignment, as the typescript file can be printed out later with lpr(1). If the argument file is given, script saves all dialogue in file. If no file name is given, the typescript is saved in the file typescript. Option: -a Append the output to file or typescript, retaining the prior contents. -c command Run the named command instead of the shell. Useful for capturing the output of a program that behaves differently when associated with a tty. -d When playing back a session with the -p flag, don't sleep between records when playing back a timestamped session. -f Flush output after each write. This is useful for watching the script output in real time. -p Play back a session recorded with the -r flag in real time. -q Be quiet, and don't output started and ended lines. -r Record a session with input, output, and timestamping. The script ends when the forked shell exits (a control-D to exit the Bourne shell (sh(1)), and exit, logout or control-d (if ignoreeof is not set) for the C-shell, csh(1)). Certain interactive commands, such as vi(1), create garbage in the typescript file. script works best with commands that do not manipulate the screen, the results are meant to emulate a hardcopy terminal. ENVIRONMENT
The following environment variable is used by script: SHELL If the variable SHELL exists, the shell forked by script will be that shell. If SHELL is not set, the Bourne shell is assumed. (Most shells set this variable automatically). SEE ALSO
csh(1) (for the history mechanism). HISTORY
The script command appeared in 3.0BSD. BUGS
script places everything in the log file, including linefeeds and backspaces. This is not what the naive user expects. BSD
October 17, 2009 BSD
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