[Bioperl-l] Error loading sequence with load_seqdatabase.pl

Duangdaow Kanhasiri dbastar at yahoo.com
Fri Jun 10 00:32:42 EDT 2005 

Thank you very much for your advice, Hilmar...

I've found that, after several times of restarting the
perl script load_seqdatabase.pl and it wouldn't run
any more with the error as: 

$perl load_seqdatabase.pl /export/Bacteria/*/*.gbk &
 [1]+  Segmentation fault      perl
load_seqdatabase.pl
 /export/Bacteria/*/*.gbk &


Finally I couldn't even run any perl command anymore
as:

$ perl --version
Segmentation fault

I've ask for help aroud here and someone told me that
the command I used might have loaded to many sequence
files names at one time that make it impossible for
the perl script load_seqdatabase.pl to handle.

I've done the work around for this problem by
re-booting the machine (in -order to make the perl
work again), and devided the genbank sequence files to
be loaded with the perl script load_seqdatabase.pl
into many small number of files and load them one
small chunk at a time.    

Now it started to run again and this time I'm praying
for it to continue working, if not, another pray is   
  that I could re-start it agin after it failed. 


Regards,

Davina


 

--- Hilmar Lapp <hlapp at gmx.net> wrote:

> First off, I wouldn't continue this thread on
> biosql-l, it's for schema 
> questions and this clearly isn't one. The script is
> a perl/bioperl 
> script and some people on the bioperl-l list may
> happen to be on a 
> platform similar to yours.
> 
> Second, you're saying now the script wouldn't run at
> all anymore? With 
> what error message? You might try to supply --debug
> as an option if the 
> script does at least something before it dies. The
> output will be 
> potentially extensive so be sure to capture in a
> file, then send it me.
> 
> If the script dies immediately I'm afraid I can't do
> anything. My gut 
> feeling is that there is something with your
> compiler, C runtime 
> library, or DBI/DBD compiled code that doesn't play
> well with your 
> perl. Did you do a binary install of perl or did you
> compile it from 
> source?
> 
> Really your best bet is to find someone who's on the
> same or a similar 
> platform and see whether he/she has had similar
> problems or none of 
> these.
> 
> 	-hilmar
> 
> On Jun 9, 2005, at 11:55 AM, Duangdaow Kanhasiri
> wrote:
> 
> > The system I use hase following configs:
> >
> > CPU:               2 @ AthlonXP2000
> > OS:                Rocks Cluster v 3.3
> > Total Memory:      2 GB
> > DBD::Pg version:   1.42
> > DBI version:       1.48
> >
> > I've attached the out put of the top command
> (top.txt)
> > with this mail.  Unfortunately that the script
> > load_seqdatabase.pl wouldn't run anymore, no
> matter
> > how many time I tried running it, therefore, I
> > couldn't measure how much it consumes the resource
> > (cpu, memory) on the machine.
> >
> > Regards,
> >
> > Davina
> >
> >
> > --- Hilmar Lapp <hlapp at gmx.net> wrote:
> >
> >> What OS are you running this on? How much memory
> >> have you got on the
> >> machine on which you run the script, and on the
> >> machine on which you
> >> run the database? Are these the same or not?
> Which
> >> version of DBI and
> >> DBD::Pg?
> >>
> >> This hasn't been reported by anyone else really
> so I
> >> suspect it's
> >> either due to too limited memory, or a problem in
> >> the DBD driver or in
> >> the DBI compiled code. Can you watch the process
> >> (using, e.g., top) and
> >> see how fast it increases in memory consumption?
> >> Since you can continue
> >> when you restart it's not something specific to
> one
> >> sequence that would
> >> trigger the problem; rather it appears whenever
> you
> >> have run through a
> >> certain number of entries the process dies.
> >>
> >> 	-hilmar
> >>
> >> On Jun 8, 2005, at 7:43 PM, Duangdaow Kanhasiri
> >> wrote:
> >>
> >>> Hi,
> >>>
> >>> I've used the bioperl script load_seqdatabase.pl
> >> (came
> >>> with the biosql' scripts) to load the bacterial
> >>> sequence in genbank format(*.gbk) into
> PostgreSQL
> >> 8.0
> >>> database on Linux machine as:
> >>>
> >>> $perl load_seqdatabase.pl
> /export/Bacteria/*/*.gbk
> >> &
> >>>
> >>> Where  under the /export/Bacteria/ path are the
> >>> Bacteria's name path e.g. Acinetobacter_sp_ADP1
> >> and
> >>> the file name are like NC_006824.gbk.
> >>>
> >>> Previously it used to load some sequences in to
> >> some
> >>> tables in biosql database (count from table
> >> bioentry)
> >>>
> >>> bioseq=# select count(*) from bioentry;
> >>>  count
> >>> -------
> >>>    33
> >>> (1 row)
> >>>
> >>>
> >>> However, after a while it then stopped with the
> >> the
> >>> error:
> >>>
> >>> [1]+  Segmentation fault      perl
> >> load_seqdatabase.pl
> >>> /export/Bacteria/*/*.gbk &
> >>>
> >>> I then checked and removed the *.gbk file that
> >> have
> >>> already been loaded in to the table, leaving
> only
> >> the
> >>> unloaded ones and ran the scripted again.  It
> >>> continued to work for some times and stopped
> >> again.  I
> >>> repeated the process several times until 173
> >> sequences
> >>> were loaded into the table:
> >>>
> >>> bioseq=# select count(*) from bioentry;
> >>>  count
> >>> -------
> >>>    173
> >>> (1 row)
> >>>
> >>> The program then stopped again and this time it
> >>> wouldn't run anymore even I tried with only on
> >> file.
> >>> The error is still the same like:
> >>>
> >>> $ perl load_seqdatabase.pl
> >>>
> >>
> >
>
/export/Bacteria/Lactobacillus_johnsonii_NCC_533/NC_005362.gbk
> >>> Segmentation fault
> >>> $
> >>>
> >>> Now I couldn't load the rest of my sequences
> into
> >> the
> >>> database anymore.  I would be very apprecialed
> if
> >> any
> >>> one knows how to solve the "Segmentation fault"
> >>> problem?
> >>>
> >>> Regards,
> >>>
> >>> Davina
> >>>
> >>>
> >>> 		
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> >
>
online.html<load_seqdatabase.pl>_______________________________________
> >>
> >>> ________
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> >>> Bioperl-l at portal.open-bio.org
> >>>
> >>
> >
>
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> >> -- 
> >>
> >
>
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> 
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