[Bioperl-l] Zombie processes with GenBank get_Seq_by_acc()

Belaid MOA belaid_moa at hotmail.com
Tue May 10 20:40:31 UTC 2011


Dear All,
  I installed the latest version of BioPerl and I ran a very simple code: it goes through each line (an ACC) in a file and uses GenBank to get the sequence
via get_Seq_by_acc(). A look at ps shows that there were a lot of zombie processes (with <defunct> attribute) created. The list grows with the time.
This means that Bio:DB:GenBank is forking and not cleaning the children. Is there any way to overcome the issue? Moreover, is there any way
to specify the number of forked processes?

With best regards,
-Belaid.
 		 	   		  



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