I am a biology person and running a program named autodock. I have some files from ZINC library in .mol2 format. As per requirement I need to split this files with the csplit command and I received all the content in my directory. The parent file was split into very very many small files. Every file name is like this: ZINC14382748.mol2. Now I have to change all these files to pdbqt format and I have to use the following script:

#!/bin/csh # # $Id: ex02.csh,v 1.5 2007/07/19 21:52:59 rhuey Exp $ 
# use the 'prepare_ligands.py' python script to create pdbq files 
cd $VSTROOT/VirtualScreening/Ligands 
foreach f (`ls *`) echo $f pythonsh ../../prepare_ligand4.py -l $f -d ../etc/ligand_dict.py end 

When I use it, it says

/bin/ls: Argument list too long

In short upon successful completion it will duplicate the above number of files into another format. So is there any reasonable solution to tackle this problem?

  • 2
    What is the command you typed? It probably contained something like ls * which will expand to all the files in your directory. If you have a lot of those files, the resulting command line is too long to process.
    – michas
    Jul 9 '16 at 3:16
  • I used the following script, and i forgot to mention that i am working on a workstation have 32G of RAM with and it says 6 cores and 12 processors with a cache size of 12288.
    – Ash
    Jul 9 '16 at 3:27
  • #!/bin/csh # # $Id: ex02.csh,v 1.5 2007/07/19 21:52:59 rhuey Exp $ # # use the 'prepare_ligands.py' python script to create pdbq files cd $VSTROOT/VirtualScreening/Ligands foreach f (ls *) echo $f pythonsh ../../prepare_ligand4.py -l $f -d ../etc/ligand_dict.py end
    – Ash
    Jul 9 '16 at 3:27
  • 2
    Please edit your question so that it has the script in it. Jul 9 '16 at 3:54
  • 1
    Try changing the loop to foreach f (./*) instead of foreach f (ls *).
    – clk
    Jul 9 '16 at 4:36
  1. Don’t parse the output of ls.  Just say foreach f (*).  Also,
  2. You should always quote your shell variable references (e.g., "$f") unless you have a good reason not to, and you’re sure you know what you’re doing.
  • Now it says, command not found. Well I think I need to recompile my kernel. Already I have change values directly in to this file, binfmts.h. Do you know how it successfully recompile it? I am using a work station with 32G of RAM.
    – Ash
    Jul 9 '16 at 7:15
  • 2
    Well, go ahead and do what you think you need to do, but I doubt that recompiling your kernel will have any effect on whether this script works. Jul 9 '16 at 7:28
  • 1
    @Ash It should not say "command not found". Please show your new script and the complete error message. Exactly what did you type to run it? Did you maybe try to use (ba)sh to run it? Try to run it explicitly with csh: csh myscript Also be aware that your problem has nothing to do with the memory of your computer or the configuration of your kernel. It is simply a bug in your script.
    – michas
    Jul 9 '16 at 9:28
  • Dear Michas, in tcsh i run it with source ex02.csh, the error is same "argument too long". In bash i ran it "./ex02.sch", the error is same "argument too long". I changed ("ls *") to ("./ *") and got an error like this, "./:Permission denied"). Also i tried your way, csh ex02.csh, error is same "argument too long"
    – Ash
    Jul 9 '16 at 10:48

The source of the problem is that you have far too many small files.

If I'm reading it right, you have over 14 million files. There is no way that ANY shell is going to be able to have over 14 million file names on the command line. Aside from that. your filenames seem to be about 18 characters long, so that's roughly 18*14M or about 252 megabytes just to hold the filenames.

bash for example, has a limit of 128KB. ever so slightly smaller than 252MB. I have no idea what limit csh has because i don't use it. It's unlikely to be any larger than bash's command-line length limit. It certainly won't be 252MB or greater.

However, all is not lost, you can use find ... -exec instead.

find . -maxdepth 1 -type f -name '*.mol2' \
  -exec pythonsh ../../prepare_ligand4.py -l {} -d ../etc/ligand_dict.py \;

This will run prepare_ligand4.py ONCE for each file, so will take a very long time. You might be able to speed it up a little (not much, not with 14+M files to process) by using find ... -print0 with xargs -0 -P ... or GNU parallel -0 ... instead of find ... -exec

A much better solution would be to download source code for prepare_ligand4.py and modify it so that you can give it one large file (e.g. the original file before csplit-ing it) and it will process each block individually. It'll be much faster and easier to work with. You'll probably still have over 14M output files (assuming that a combined output file would be useless...if it isn't you're in luck!), but that's better than having 14M input files AND 14M output files.

This would, of course, require some skill with python programming.

Maybe someone has already encountered the same problem and written their own enhanced version of prepare_ligand4.py. It's worth spending some time searching, or maybe try the Autodock Forum or even contact the Autodock author.

  • 2
    The 128kB limit is not a bash limit, it's a kernel limit. Bash can handle command lines that are as long as memory allows, but they have to be calls to builtins or functions. Contrast bash -c 'echo {1..999999} >/dev/null' with bash -c '/bin/echo {1..999999} >/dev/null' Jul 9 '16 at 22:34

You obviously has a lot of files. Consider using GNU Parallel http://www.gnu.org/software/parallel/ The 'ls -U' does not sort the files and then it is faster.

cd $VSTROOT/VirtualScreening/Ligands
ls -U ZINC* | parallel echo {} \; pythonsh ../../prepare_ligand4.py -l {} -d ../etc/ligand_dict.py

I don't understand why you echo it. Do you parse it on to a new script? My guess is that 'prepare_ligand4.py' is the script for conversion and then this should do the job (in parallel):

cd $VSTROOT/VirtualScreening/Ligands
ls -U ZINC* | parallel pythonsh ../../prepare_ligand4.py -l {} -d ../etc/ligand_dict.py
  • Yes man i have 24 Million files but that is good that all of them are zipped in different files and each of that contain like 1,36,000 files. Sorry I am not good in computer stuffs, my friends helped me and he changed the csh for me to bash. So if you mean i can run it very fast, i will be happy to see and try your script :P. Most of the things are out of my box you explained above. Cheers @hschou
    – Ash
    Jul 9 '16 at 11:43
  • Your script will only process one file at the time so it will take a long time for you process. Install GNU Parallel to use all your cores in parallel.
    – hschou
    Jul 9 '16 at 14:46

I have solved the problem, let me share with you. I Rename the bash.csh to bash.sh, Next I change my script in order to run it in bash. Here is my new script to help in future for the same issue.

cd $VSTROOT/VirtualScreening/Ligands/
for f in ZINC*.mol2
    echo "$f"
    pythonsh ../../prepare_ligand4.py -l "$f" -d ../etc/ligand_dict.py

For a beginner like me, here ZINC is a part of name present in all of the ligand names, so must keep according to your ligand name. Thanks for you time and my friend here who helped me passionately.

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