Indeed such a warning is harmless, and in the log you sent it seems all the macros ended successfully.
But I noticed, in the digi:
===================================================
PndEmcHitsToWaveform::FinishTask
***************************************************
Read Hits# -1717986919
Produc waveforms# 0
***************************************************
=========================================================
PndEmcWaveformToDigi::FinishTask
=========================================================
Total waveforms# 0
Total expected hits# 0
Total fpga hits# 0
Total digis Above th. #0, threshold# 0.002
=========================================================
PndEmcMakeCluster::FinishTask
*********************************************************
Read digis# 0
Produce cluster# 0
*********************************************************
=================================================
PndEmcExpClusterSplitter::FinishTask
=================================================
read digis #0
=================================================
PndEmcPhiBumpSplitter::FinishTask
=================================================
-I- PndDrcHitProducerReal: Finish
-------------------- GEM Digitizer : Summary ------------------------
Events: 0
MC Points: 0 ( -nan per event )
Digis: 0 ( -nan per event )
--> ( -nan per sensor )
--> ( -nan% occupancy )
--> ( 2 x -nan per point )
---------------------------------------------------------------------
-------------------- GEM Hit Finder : Summary -----------------------
Events: 0
Digis: 0 ( -nan per event )
HitsTemp: 0 ( -nan per event )
Hits: 0 ( -nan per event )
--> ( -nan per sensor )
--> ( -nan per digi )
---------------------------------------------------------------------
>>> HF >>> prep time = 0s (get data from input)
>>> HF >>> sort time = 0s (sort clusters, 0)
>>> HF >>> create time = 0s (create hits, 0)
>>> HF >>> confirm time = 0s (confirm hits, 0)
>>> HF >>> activ. time = 0s (activate digis, 0)
>>> HF >>> all time = 0s (all time spent in Exec, 0)
---------------------------------------------------------------------
It seems no digits/hits are created. I think you are messing up something in the sim or in the digi.
Afterwards, in the reco:
[INFO ] The number of entries in the tree is 0
[INFO ] FairRootManager::ReadEvent(0): The tree has 0 entries
The digi tree is empty (maybe also the sim).
Last comment: you should stream also the errors! If not you are cutting out from the log all the error messages:
root -l -q xxX.C >> output.txt 2>&1 &