UNIX for Beginners Questions & Answers

/path/to/${ID}*/path/to/folder (always this format)

# Set an array in one step in bash
array=( $(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' list | tr -d '\r') )  ## match run with samples
echo "This is array" "$array" > /tmp/out

This is array ID1

# Set an array in one step in bash
array=( $(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' "$run_dir"/rna.barcodes | tr -d '\r') )  ## match run with samples
   for file in "${array[@]}" ; do
    echo "This is array" "$file" > /tmp/loop.out
done

This is array ID2

tree -d
.
├── D1
│   ├── D2
│   │   └── L1
│   ├── D3
│   │   └── L2
│   └── D4
│       ├── L1
│       ├── L2
│       └── L3
└── test
    └── D1
        └── D3
            ├── L1
            └── L2

14 directories

├──/path/to/
│   ├── ${ID}*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID/folder
│   ├── ${ID}*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID/folder

# Set run array
array=( $(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' list | tr -d '\r') )  ## match run in rna.barcode and extract patient

# iterate through array
for ID in "${array[*]}" ; do
echo "$ID" > /tmp/out.txt
       echo "( cd /path/to/${ID}*/path/to/folder && xec sshpass -f file.txt scp -- *.png* xxx@xxx.xx.xx.xxx:/path/to/destination/${ID}-cn_results)"
       sshpass -f out.txt ssh -o strictHostKeyChecking=no -t xxx@xxx.xx.xx.xx
done

ID1 ID2

( cd /path/to/ID1 ID2*/*/path/to/folder && exec sshpass -f file.txt scp -- *.png* xxx@xxx.xx.xx.xxx:/path/to/destination/ID1 ID2-cn_results.png)

├──/path/to/   ---- common path after ssh ---
│   ├── ID1*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID1/folder
│   ├── ID2*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID2/folder
Description:

After ssh to the common path on the server, each unique ID is used to further navigate to folder. In each folder there is a png (cn_results), that the unique ID is append to (ID-cn_results) and this 
append file is scp to xxx@xxx.xx.xx.xxx:/path/to/destination. It seems that since array is one line both are being used and that is causing the error?

OLDIFS="$IFS"
IFS="."

...

IFS="$OLDIFS"