Hi,
I tried it with 2002 input files and it runs fine.
I think it it may be your really long file paths.
There is some limit in the shell to the number of characters that can be used as an argument.
Not sure what that is, but you may be running into that limit.
I think moving your data to a folder with a shorter path may be painful.
So maybe try modifying your csv file to remove this part of the path from each line (find / replace will be your friend):
/media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/
Then go to that folder:
cd /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/
And run @ClustExp_CatLab from that folder.
So 3dcopy will not have such a long argument list.
Let me know if that works.
If not, we can try something else.
thanks, Justin