On Sun, 11 Aug 2019 at 23:18, Stephen P. Molnar <s.mol...@sbcglobal.net> wrote: > > I am running an up-to-date installation of Buster on my Linux platform > and have run into a strange problem with a bash script.
[...] > for d in $(cat ligand.list) This line is the problem, it is vulnerable to various kinds of breakage and is therefore bad practice, see here: http://mywiki.wooledge.org/DontReadLinesWithFor Try this instead, it is the recommended practice and it may well solve your \r issue: #!/bin/bash while IFS= read -r d do cd "${d}_apo-3k9b" echo "${d}apo-3k9b" echo "${d}apo-3k9b.dpf" /home/comp/Apps/Autodock/autodock4 -p "${d}apo-3k9b.dpf" -l "${d}apo-3k9b.dlg" cd .. done <ligand.list
