#768 error in similarity search

[Laszlo Jicsinszky]

OS: Windows 7, 64 bit, OB 2.3.1

a) Minor, and affect the help file and the extraction of first file. The ChEMBLdb current version (11) is > 2 GB, and the extraction method for Windows in not working anymore (a shortcut might be using the type command, output to file and break immediately, then the output file can be opened by even notepad)

b) Major, affect the usage.
Testing the similarity search, and followed the suggested way in help, I have encountered the following problems:

b.1.) using command babel:

L:\pgm\openbabel>babel chembl_11.sdf mostsim.sdf -s firstmol.sdf -at5

*** Open Babel Error in OpenBabel::VF2Mapper::MapGeneric
time limit exceeded...

output file length=0, and babel seems to hang up working, prompt has not been back

b.2) It is recommended to use obabel instead of babel.
typing obabel (recommended) instead of babel I got the following message

L:\pgm\openbabel>obabel chembl_11.sdf mostsim.sdf -s firstmol.sdf -at5
Missing or unknown output file or format spec or possibly a misplaced option.
Options, other than -i -o -O -m, must come after the input files.

Open Babel 2.3.1 -- Oct 9 2011 -- 17:57:01
Usage:
obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]

Try -H option for more information.

[Noel O'Boyle]

(a) What command-line did you use? It works for me on Windows.

(b1) I think you need to wait longer.

(b2) You need to read the docs for obabel. There are some differences compared to babel. For example, it requires "-O outputfilename".

[Laszlo Jicsinszky]

Thanks a lot.

(a) What command-line did you use? It works for me on Windows.

I used windows 7 64bit. As the first row says in my comment. As far as I know in windows only one command prompt exists (except the superuser mode, which is the same),
But I tried linux (salix64) also but custom user installation was not successful (it was successful but the use was buggy) and my own build failed, I dropped it for better times.

(b1) I think you need to wait longer.
I think ~ 1hr waiting is enough long on a Athlon X4 2.9 GHz machine.

(b2) You need to read the docs for obabel.
As I wrote, I tried to follow the help. In that is recommended to use obabel instead of babel, but perhaps I did not dig too deep.
BTW: you recommend to read documentation, but what would you do when you are reading the followings (see my original post):

"Options, other than -i -o -O -m, must come a f t e r the input files."
Next lines:
"Usage:
obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]"

In the first, in/output type should f o l l o w the files, the second shows should be b e f o r e the files. Which one is true ?

I have tried both but with same results.