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Syntax error running command from a script

I have a problem running one command from a file.

When I execute command directly in terminal everything is working and software do it well. If I try to run it from the file, there is error with one file all the time.

If I run it directly in terminal with this command and full paths it is working:

/home/lukas/snap/bin/gpt /home/lukas/Desktop/automatic/test/resample_s2.xml -e -p /home/lukas/Desktop/automatic/test/resample_20m.properties -t  "/home/lukas/Desktop/automatic/outputs/processed.dim" /home/lukas/Desktop/automatic/inputs/S2A_MSIL2A_20170717T095031_N0205_R079_T34UCV_20170717T095631.SAFE/MTD_MSIL2A.xml 
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When I run this command from a script, it throws an error with …

command-line bash

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