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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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Zombie process is generated when run LTR.identifier.pl #50

Closed forrwill closed 5 years ago

forrwill commented 5 years ago

Hi Shujun,

   I found some  process  become zombie process when I had been run it a long time;

There are partly result of command top :

SN Jul11 0:00 \_ sh -c perl /bin/LTR.identifier.pl final.fasta ... Sl Jul11 393:51 \_ perl /bin/LTR.identifier.pl final.fasta ... Z Jul12 0:00 \_ [perl] <defunct> Z Jul12 0:01 \_ [perl] <defunct> Z Jul12 0:01 \_ [perl] <defunct> Z Jul12 0:01 \_ [sh] <defunct> Z Jul12 0:01 \_ [perl] <defunct> Z Jul12 0:01 \_ [perl] <defunct> Z Jul12 0:01 \_ [perl] <defunct>

   I ran two different data, both of which will be stuck in these states(Z).

Can you give some advice to avoid such problems? should I use single thread? Thanks!

oushujun commented 5 years ago

Hello,

If you can see new data are generating to the .defalse file, then they are probably fine. Otherwise you may have allocated more threads than your system currently has and the multithreading module is stuck in this. For this situation you need to cancel and rerun it with less threads, say, 10 works very well for me.

Shujun

On Wed, Jul 17, 2019, 12:45 AM Will notifications@github.com wrote:

Hi Shujun,

I found some process become zombie process when I had been run it a long time; There are partly result of command top ; `SN Jul11 0:00 sh -c perl /bin/LTR.identifier.pl final.fasta ... Sl Jul11 393:51 perl /bin/LTR.identifier.pl final.fasta ...

Z Jul12 0:00 [perl] Z Jul12 0:01 [perl] Z Jul12 0:01 [perl] Z Jul12 0:01 [sh] Jul12 0:01 [perl] Z Jul12 0:01 [perl] Z Jul12 0:01 _ [perl] `

I ran two different pieces of data and it will be stuck in these states; should I use single thread? Can you give some advice to avoid such problems?

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forrwill commented 5 years ago

Hi Shujun, Thanks a lot, .defalse file stopped updating, in the server used before, there are too many tasks competing for resources; I will try to reduce the thread and run on a server with sufficient resources