I admit I did not fully understand your code and did run it as you had had it. That is how I got the No Translation Found. I only removed the suffix lines as I though that was I thought that was referring to $1 in input, and since it didn't match No Translation Found. I was mistaken and hope the below helps.

Files in directory being updated in dir: R_2016_09_21_14_01_15_user_S5-00580-9-Medexome

Code:

IonXpress_007.bam
IonXpress_007.vcf
IonXpress_007.bam.bai
IonXpress_008.bam
IonXpress_008.vcf
IonXpress_008.bam.bai
IonXpress_009.bam
IonXpress_009.vcf
IonXpress_009.bam.bai

input

Code:

IonXpress_001 MEC2
IonXpress_002 MEC3
IonXpress_003 MEV48
R_2016_10_21_09_52_37_user_S5-00580-10-Medexome

IonXpress_007 MEV21
IonXpress_008 MEV22
IonXpress_009 MEV23
R_2016_09_21_14_01_15_user_S5-00580-9-Medexome  --- line matches dir

The identifier is in $2 of the input file. That is what the file in dir should be updated with. The $1 value will match the file name (before it is renamed).

So using the dir in the example:

Code:

MEV21.bam
MEV21.vcf
MEV21.bam.bai
MEV22.bam
MEV22.vcf
MEV22.bam.bai
MEV23.bam
MEV23.vcf
MEV23.bam.bai

Each filename in dir [ICODE]IonXpress_007,IonXpress_008,IonXpress_009 will match a $1 value in input. The corresponding $2 value is what the filename in dir is renamed to. The dir will match only one line string appears in the input file and the 3 lines above it have the identifiers in it. Thank you very much .