Hi,

Code:

NEWEST=`ls -tr1d "${MY_DIR}/"*.${FILEEXT} 2>/dev/null | tail -1`

Above code is not doing what you explained in your post.

You need to read line by line in out.txt file then find / list the files with *.bam extension , copy etc.

It may be done in oneliner , if you can add more description about structure of Folder1,Folder2 and /home/cmccabe/nfs/exportedReports with clear example.

if not, try like this:

Code:

cat out.txt
DIR1
DIR2
$ ls -a DIR1/
.  ..  123.bam  abc.bam  xyz.log
$ ls -a DIR2/
.  ..  cool.txt  me.bam

Sample code written here to update your script.

Code:

a=/home/cmccabe/nfs/exportedReports;DEST="/home/cmccabe/Desktop/NGS/API/$DATE";
while read line; do find $a/$line -name "*.bam" -exec cp {} $DEST \;
done < out.txt 
$ ls -a $DEST
.  ..  123.bam  abc.bam  me.bam