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Full Discussion: Cp command works on command line but not in bash
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.
This User Gave Thanks to Corona688 For This Post:
cmccabe
 

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LEARN ABOUT DEBIAN

pycocuma

pycocuma(1)							    Addressbook 						       pycocuma(1)

NAME

       pycocuma - Pythonic Contact and Customer Management

SYNTAX

       pycocuma [options] [connection-string]

DESCRIPTION

       PyCoCuMa  (Pythonic Contact and Customer Management) provides a personal information system for addresses, telephone numbers and other data
       associated with personal contacts (also supports photographic pictures).

       PyCoCuMa is purely written in Python with a Tk graphical interface. PyCoCuMa is based on an XML-RPC client-server architecture. The  server
       stores  its  data  in  compatible vCard (ver. 3.0) files (*.vcf) which can be read by all modern address programs (Evolution, KAddressbook,
       Outlook, GnomeCard, etc).

       This manpage documents the PyCoCuMa client (which can also run standalone).

OPTIONS

       connection-string
	      addressbook filename / server url

       -h --help
	      show help

       -c --config
	      location of configuration file (default: ~/.pycocuma)

       --noconf
	      do not save configuration / preferences

       -t --type
	      connection type: xmlrpc or file (default: file)

       --finder
	      open QuickFinder

       --import
	      import from file/stdin (-) (e.g. vcard:/tmp/John.vcf)

       --export
	      export to file or stdout (e.g. latex:-)

EXAMPLES

       pycocuma --type=xmlrpc http://localhost:8810

       pycocuma --config=/tmp/pycocumatest.conf --type=file ./addressbook.vcf

AUTHORS

       PyCoCuMa was written by Henning Jacobs.

       This manpage was written by Christoph Berg for the Debian GNU/Linux distribution (but may be used by others).

SEE ALSO

       PyCoCuMa home page
	      http://www.srcco.de/pycocuma/

       pycocuma-server(1)

Debian								      0.4.5-5							       pycocuma(1)
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