[BioSQL-l] Re: [Bioperl-l] Error loading sequence with
load_seqdatabase.pl
Duangdaow Kanhasiri
dbastar at yahoo.com
Wed Jun 8 23:55:57 EDT 2005
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>_______________________________________
>
> > ________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> >
>
http://portal.open-bio.org/mailman/listinfo/bioperl-l
> --
>
-------------------------------------------------------------
> Hilmar Lapp email: lapp
> at gnf.org
> GNF, San Diego, Ca. 92121 phone:
> +1-858-812-1757
>
-------------------------------------------------------------
>
>
>
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-------------- next part --------------
[root at biogenome root]# top
10:31:14 up 27 days, 21:20, 5 users, load average: 0.00, 0.02, 0.03
193 processes: 192 sleeping, 1 running, 0 zombie, 0 stopped
CPU states: cpu user nice system irq softirq iowait idle
total 1.8% 0.0% 0.0% 0.0% 0.0% 0.0% 198.0%
cpu00 1.9% 0.0% 0.0% 0.0% 0.0% 0.0% 98.0%
cpu01 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 100.0%
Mem: 2057220k av, 1556640k used, 500580k free, 0k shrd, 167096k buff
1101048k actv, 266692k in_d, 39936k in_c
Swap: 4192956k av, 91620k used, 4101336k free 1196752k cached
PID USER PRI NI SIZE RSS SHARE STAT %CPU %MEM TIME CPU COMMAND
16683 root 23 0 1288 1288 844 R 1.9 0.0 0:00 0 top
1 root 15 0 520 516 456 S 0.0 0.0 0:29 0 init
2 root RT 0 0 0 0 SW 0.0 0.0 0:00 0 migration/0
3 root RT 0 0 0 0 SW 0.0 0.0 0:00 1 migration/1
4 root 15 0 0 0 0 SW 0.0 0.0 0:00 1 keventd
5 root 34 19 0 0 0 SWN 0.0 0.0 0:00 0 ksoftirqd/0
6 root 34 19 0 0 0 SWN 0.0 0.0 0:00 1 ksoftirqd/1
9 root 15 0 0 0 0 SW 0.0 0.0 0:00 0 bdflush
7 root 15 0 0 0 0 SW 0.0 0.0 0:37 0 kswapd
8 root 15 0 0 0 0 SW 0.0 0.0 0:24 0 kscand
10 root 15 0 0 0 0 SW 0.0 0.0 0:19 0 kupdated
11 root 25 0 0 0 0 SW 0.0 0.0 0:00 0 mdrecoveryd
17 root 25 0 0 0 0 SW 0.0 0.0 0:00 1 scsi_eh_0
18 root 25 0 0 0 0 SW 0.0 0.0 0:00 1 aacraid
20 root 25 0 0 0 0 SW 0.0 0.0 0:00 1 scsi_eh_0
23 root 15 0 0 0 0 SW 0.0 0.0 1:29 1 kjournald
70 root 25 0 0 0 0 SW 0.0 0.0 0:00 0 khubd
1165 root 15 0 0 0 0 SW 0.0 0.0 0:49 0 kjournald
1418 root 15 0 0 0 0 SW 0.0 0.0 0:00 1 eth0
1543 root 15 0 620 608 524 S 0.0 0.0 0:59 0 syslogd
1547 root 15 0 484 424 420 S 0.0 0.0 0:00 0 klogd
1557 root 15 0 456 448 392 S 0.0 0.0 2:04 0 irqbalance
1565 rpc 15 0 572 548 500 S 0.0 0.0 0:00 0 portmap
1584 rpcuser 25 0 716 632 628 S 0.0 0.0 0:00 1 rpc.statd
1595 root 15 0 404 388 344 S 0.0 0.0 0:06 0 mdadm
1619 root RT 0 556 456 424 S 0.0 0.0 0:16 1 auditd
1629 nobody 15 0 1180 1016 724 S 0.0 0.0 24:57 1 gmetad
1658 root 15 0 472 424 400 S 0.0 0.0 0:01 0 pvfsd
[root at biogenome DBD]# df -h
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 5.8G 3.6G 1.9G 66% /
/dev/sda3 125G 24G 95G 21% /export
none 1005M 0 1005M 0% /dev/shm
tmpfs 503M 3.5M 499M 1% /var/lib/ganglia/rrds
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