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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 SUNOS

cachefslog

cachefslog(1M)						  System Administration Commands					    cachefslog(1M)

NAME

       cachefslog - Cache File System logging

SYNOPSIS

       cachefslog [-f logfile | -h]  cachefs_mount_point

DESCRIPTION

       The  cachefslog	command displays where CacheFS statistics are being logged. Optionally, it sets where CacheFS statistics are being logged,
       or it halts logging for a cache specified by cachefs_mount_point. The cachefs_mount_point argument is a mount point of a cache file system.
       All file systems cached under the same cache as cachefs_mount_point will be logged.

OPTIONS

       The following options are supported. You must be super-user to use the -f and -h options.

       -f logfile      Specify the log file to be used.

       -h	       Halt logging.

OPERANDS

       cachefs_mount_point     A mount point of a cache file system.

USAGE

       See largefile(5) for the description of the behavior of cachefslog when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes).

EXAMPLES

       Example 1: Checking the Logging of a directory.

       The example below checks if the directory /home/sam is being logged:

       example% cachefslog /home/sam
       not logged: /home/sam

       Example 2: Changing the logfile.

       The example below changes the logfile of  /home/sam to /var/tmp/samlog:

       example# cachefslog -f /var/tmp/samlog /home/sam
       /var/tmp/samlog: /home/sam

       Example 3: Verifying the change of a logfile.

       The example below verifies the change of the previous example:

       example% cachefslog /home/sam
       /var/tmp/samlog: /home/sam

       Example 4: Halting the logging of a directory.

       The example below halts logging for the /home/sam directory:

       example# cachefslog -h /home/sam
       not logged: /home/sam

EXIT STATUS

       The following exit values are returned:

       0	       success

       non-zero        an error has occurred.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWcsu			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       cachefsstat(1M), cachefswssize(1M), cfsadmin(1M), attributes(5), largefile(5)

DIAGNOSTICS

       Invalid path    It is illegal to specify a path within a cache file system.

SunOS 5.10							    7 Feb 1997							    cachefslog(1M)
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