On 8/11/19, David <bouncingc...@gmail.com> wrote:
> On Mon, 12 Aug 2019 at 01:07, Stephen P. Molnar <s.mol...@sbcglobal.net>
> wrote:
>>
>> Thanks for the suggestion.
>> However,
>> comp@AbNormal:~/Apps/Models/1-PhosphorusLigands/Acetylcholinesterases/3K9B/Results$
>> ./Run.ligand.list.sh
>> ./Run.ligand.list.sh: line 4: cd: $'Acetylcholine\r_apo-3k9b': No such
>> file or directory
>
> The form of that error message indicates that
> the directory name attempted as a result of
> this substitution
> cd "${d}_apo-3k9b"
>
> contains a carriage return (\r) character.
>
> Here's a demonstration:
>
> [david@kablamm junk]$ cd foo$'\r'foo
> bash: cd: $'foo\rfoo': No such file or directory
>
> The $'\r' in my input command is a carriage return
> character.
> Note the identical form of quoting in my error message
> and your error message.
> The $'foo\rfoo' in the error message is a carriage
> return character between two strings 'foo'.
>
> If the mysterious carriage return character is not
> in your ligand.list file, then it must be in
> your Run.ligand.list.sh file just before the underscore
> in the line
> cd "${d}_apo-3k9b"
>
> Have a look at your script file using
> 'cat -v Run.ligand.list.sh'
> The effect of cat -v is to show control characters.
>
> If possible, use an editor that can show control characters.
> If not available, you can edit that line in your script file in a way
> that would remove an invisible character in the suspect position.Or you could try doing dos2unix ligand.list dos2unix Run.ligand.list.sh and see if that gets rid of the embedded \r Lee
