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System commands not executing

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System commands not executing Perl Programming forum discussing coding in Perl, utilizing Perl modules, and other Perl-related topics. Perl, the Practical Extraction and Reporting Language, is the choice for many for parsing textual information.

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  #1  
Old May 6th, 2008, 11:34 AM
lokisapocalypse lokisapocalypse is offline
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System commands not executing
Hello all,

I have inherited a Perl script that executes several system commands:

Code:
mkdir /tmp/n3Z7
chmod 777 /tmp/n3Z7

hmmsearch --cut_tc /AMP-binding.hmm /outfiles/OUT_afumigatus.input > /tmp/n3Z7/hmm_AMP.out
hmmsearch --cut_tc /Acyl_transf_1.hmm  /outfiles/OUT_afumigatus.input > /tmp/n3Z7/hmm_Acyl_transf.out
hmmsearch --cut_tc /Condensation.hmm /outfiles/OUT_afumigatus.input > /tmp/n3Z7/hmm_Condensation.out

rm -rf /tmp/n3Z7


For some reason, the hmmsearch functions are no longer being executed but the mkdir and chmod commands work correctly. Could it be that the daemon user (which is executing these commands) does not have sufficient privileges to execute the hmmsearch command?
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  #2  
Old May 6th, 2008, 02:33 PM
awatson awatson is offline
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Yes, it could be. Or something else wrong with hmmsearch - have you tried running the commands yourself or looking in the error logs?
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  #3  
Old May 6th, 2008, 03:42 PM
lokisapocalypse lokisapocalypse is offline
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Quote:
Originally Posted by awatson
Yes, it could be. Or something else wrong with hmmsearch - have you tried running the commands yourself or looking in the error logs?


Sorry, I should have added that executing the commands through a command prompt works fine.
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  #4  
Old May 6th, 2008, 04:14 PM
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There's no Perl in what you've posted. What OS are you on - I can move this to Linux/Unix help as appropriate.
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  #5  
Old May 6th, 2008, 04:16 PM
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Orkut
can you log in as the daemon user and see what happens when you run them on the command line?

Did the logs show up anything?
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  #6  
Old May 6th, 2008, 04:17 PM
awatson awatson is offline
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Well, his perl script is using "system()" to call those commands.

Seems like a permissions problem then - can you try changing owner or permissions on hmmsearch to see if that works?
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  #7  
Old May 6th, 2008, 06:40 PM
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it'd be best to find out what the actual issue is before changing permissions, hence asking him to logon as the daemon user to see what feedback the OS gives him on the issue, or if it's possible to pipe the STDOUT and STDERR for the cron job to a text file and see if that yields any further information ... or using backticks or the qx operator to run the shell commands

perl Code:
Original - perl Code 
  1. open LOG, ">logfile.txt";
  2. @results1= qx|command1|;
  3. for (@results1) {
  4.   print LOG $_;
  5. }
  6. @results2= qx|command2|;
  7. for (@results1) {
  8.   print LOG $_;
  9. }
  10. close LOG;
Last edited by Axweildr : May 6th, 2008 at 06:42 PM.
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  #8  
Old May 7th, 2008, 07:25 AM
lokisapocalypse lokisapocalypse is offline
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I have confirmed that it is a permissions issue. Thanks for all your input.
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Old May 7th, 2008, 02:01 PM
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can you be more specific, had the user profile changed, or did somebody 'do nothing', the old "It weren't me..." defense ...
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Old May 7th, 2008, 02:04 PM
lokisapocalypse lokisapocalypse is offline
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I executed the commands in PHP which gave a return code of 127 which I assumed meant insufficient permissions. However, upon further investigation the problem was that the web browser did not know the correct path to the hmmsearch function. Thus, changing hmmsearch to /usr/local/bin/hmmsearch resolved this issue.

In other words, it had absolutely nothing to do with Perl :-)
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  #11  
Old May 7th, 2008, 02:07 PM
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the browser?? I think you meant the server, there was probably a chdir or cd command above the hmmsearch calls that was obliterated, or the search path used to contain the path to the directory that contains hmmsearch.

Whether is the shell or perl, it still needs to know where stuff is to execute it
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