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Top Forums Shell Programming and Scripting Cp command works on command line but not in bash Post 302990896 by Corona688 on Thursday 2nd of February 2017 12:09:00 PM
Old 02-02-2017
You are not capturing the errors. Try:

Code:
logfile=/home/cmccabe/Desktop/test/process.log
for file in /home/cmccabe/Desktop/test/vcf/overall/stats/*.vcf ; do
     echo "Start annovar creation: $(date) - file: $file"
     echo ${file##*/} >> /home/cmccabe/Desktop/NGS/annovar/target.txt
     cp /home/cmccabe/Desktop/test/vcf/overall/stats/*.vcf /home/cmccabe/Desktop/NGS/annovar
     echo "End annovar file creation: $(date) - file: $file"
done 2>&1 >> "$logfile"

Also: Why are you copying every single file every loop? If you're trying to copy them one at a time, cp * destination/ isn't the way to do it.
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RBASH(1)						      General Commands Manual							  RBASH(1)

NAME
rbash - restricted bash, see bash(1) RESTRICTED SHELL
If bash is started with the name rbash, or the -r option is supplied at invocation, the shell becomes restricted. A restricted shell is used to set up an environment more controlled than the standard shell. It behaves identically to bash with the exception that the follow- ing are disallowed or not performed: o changing directories with cd o setting or unsetting the values of SHELL, PATH, ENV, or BASH_ENV o specifying command names containing / o specifying a file name containing a / as an argument to the . builtin command o specifying a filename containing a slash as an argument to the -p option to the hash builtin command o importing function definitions from the shell environment at startup o parsing the value of SHELLOPTS from the shell environment at startup o redirecting output using the >, >|, <>, >&, &>, and >> redirection operators o using the exec builtin command to replace the shell with another command o adding or deleting builtin commands with the -f and -d options to the enable builtin command o using the enable builtin command to enable disabled shell builtins o specifying the -p option to the command builtin command o turning off restricted mode with set +r or set +o restricted. These restrictions are enforced after any startup files are read. When a command that is found to be a shell script is executed, rbash turns off any restrictions in the shell spawned to execute the script. SEE ALSO
bash(1) GNU Bash-4.0 2004 Apr 20 RBASH(1)
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