Hi Jason,
I have read your discussion with Michele regarding my
error report in A24 Amber tutorial.
Let me remind you the subject of error when doing A24 tutorial:
➜ ~ cd $FEW
➜ ~FEW pwd
/home/shokhen/amber14/AmberTools/src/FEW
➜ ~FEW perl $FEW/FEW.pl MMPBSA /home/shokhen/tutorial/cfiles/leap_am1
#####################################################
# #
# FEW #
# Free Energy Workflow #
# #
#####################################################
Checking input parameters and files.
sh: 1: Syntax error: Bad fd number
Cannot open file log.txt for reading.
You asked:
>I couldn't tell from looking at the FEW directory where this script is --
>do you know which script this is?
I suggest that the problem file is FEW.pl
that locates in a standard AmberTools 14 path:
/home/shokhen/amber14/AmberTools/src/FEW/FEW.pl
I would appreciate you help in problem solution.
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
On Sun, Mar 22, 2015 at 10:22 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Sun, Mar 22, 2015 at 2:19 PM, Michele Bonus <michele.bonus.hhu.de>
> wrote:
>
> > Dear Michael,
> >
> > most probably this issue has its cause in Ubuntu's use of dash (Debian
> > Almquist Shell) rather than bash or csh as the default shell.
> >
> > You could try to check the symlink of ~bin/sh, by either
> > ls -l /bin/sh
> > which might return "/bin/sh -> dash*"
> > or
> > file /bin/sh
> > which might return "/bin/sh: symbolic link to `dash'".
> >
> > If the symlink is set to dash for your system, you could alter this to
> > bash by
> > ln -sf /bin/bash /bin/sh
> >
>
> I would suggest against this. Ubuntu and Debian have good reasons for
> using dash as the default shell, specifically the fact that it is much
> lighter-weight and reduces the footprint of many components of the init
> system, like openrc or systemd (and has other advantages; for instance,
> "shellshock" did not affect Ubuntu systems, since the exploited
> vulnerability was the on-POSIX part of bash [1]).
>
> T
> he appropriate fix is in the script that is not POSIX sh-compliant.
> Either fix the script to comply with the standard, or change the shebang
> line to call bash explicitly. None of our programs should require users to
> do something that substantially alters their core OS.
>
> I couldn't tell from looking at the FEW directory where this script is --
> do you know which script this is?
>
> Thanks,
> Jason
>
> [1] http://en.wikipedia.org/wiki/Shellshock_%28software_bug%29
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Mar 23 2015 - 05:00:03 PDT
