Your link command is wrong I think
ln -s /Data/bcj/INPTA/Pipeline_Tests/Test02/J2145-0750_bm3_pa_750_100_8_22may2018.raw
./J2145-0750_58260.12269MJD_500.000MHz_29472MiB.gptool.gpt.dat
gptool produces an output in WD and you are overwriting that by
linking to raw data file ?
Your link command is wrong I think ln -s /Data/bcj/INPTA/Pipeline_Tests/Test02/J2145-0750_bm3_pa_750_100_8_22may2018.raw ./J2145-0750_58260.12269MJD_500.000MHz_29472MiB.gptool.gpt.dat gptool produces an output in WD and you are overwriting that by linking to raw data file ?