Dear Zaixu,
I upgraded my op to Ubuntu 16, when I run the PANDA, it failed with the following message:

Log of the (matlab) job : dcm2nii_dwi_00002
Started on 07-Sep-2016 15:37:13
User: W
host :W-HP-Z240-Tower-Workstation
system : unix
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The job starts now !
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1

cp: target '/home/yw/Documents//00002//tmp/test_00002_DWI_01.nii.gz' is not a directory
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Checking outputs
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The output file or directory /home/w/Documents/00002/tmp/test_00002_bvals_01 was successfully generated!
The output file or directory /home/w/Documents/00002/tmp/test_00002_bvecs_01 was successfully generated!
The output file or directory /home/w/Documents/00002/tmp/test_00002_DWI_01.nii.gz has not been generated!
The output file or directory /home/w/Documents/00002/tmp/OutputDone/dcm2nii_dwi_00002.done was successfully generated!
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07-Sep-2016 15:37:13 : The job has FAILED
Total time used to process the job : 0.04 sec.
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Any suggestions?

Thanks,
Yawu