Replacement string not working in GNU parallel - gnu-parallel

Question

I have the script run_md.py which produces the file test.dcd from the input file named test.pdb.
I want to execute the same command on multiple input files (test*.pdb) on a remote server using GNU parallel and transfer the result back to the local computer. Therefore, I'm using the following command:
parallel --trc {.}.dcd -j 2 -S $SERVER1 './run_md.py {} 1000' ::: test*.pdb
The command is running as expected on the server using 2 slots. However, the files are not transferred back and I get the following error:
rsync: link_stat "/home/bougui/{.}.dcd" failed: No such file or directory (2)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1655) [Receiver=3.1.1]
It looks like the replacement string is not working. How can I make it works?
Below is the output of parallel --version:
GNU parallel 20130922
Copyright (C) 2007,2008,2009,2010,2011,2012,2013 Ole Tange and Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
GNU parallel comes with no warranty.
Web site: http://www.gnu.org/software/parallel
When using GNU Parallel for a publication please cite:
O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.

Answer 1

What you are doing is 100% correct. So something on your system is breaking this. Please try this on another system and if possible follow REPORTING BUGS from man parallel.

Answer 2

The bug reported in that thread has been fixed and this feature works well with the latest version of GNU parallel (20160622). The GNU parallel version 20130922 packaged with Debian 8.5 is buggy for the usage of {.} string replacement, as described below:
With more test I found that the output file must be specified with a replacement string in the command run in parallel.
For testing purpose, you can find below a complete example that others can run:
echo This is input_file > input_file && parallel --trc {}.out -S $SERVER1 cat {} ">"{}.out ::: input_file
The example above works well. When I use the substitution string {.} as below:
echo This is input_file > input_file.in && parallel --trc {.}.out -S $SERVER1 cat {} ">"{.}.out ::: input_file
It works, as well. However, if I didn't specify {.}.out in the command run in parallel as below:
echo This is input_file > input_file.in && parallel --trc {.}.out -S $SERVER1 cat {} ">"input_file.out ::: input_file
... I reproduce the error:
rsync: link_stat "/home/bouvier/{.}.out" failed: No such file or directory (2)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1655) [Receiver=3.1.1]
rsync: [Receiver] write error: Broken pipe (32)
Therefore the output file must be specified in the command run in parallel.