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

Duangdaow Kanhasiri dbastar at yahoo.com
Wed Jun 8 07:43:41 EDT 2005


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;
(1 row)

However, after a while it then stopped with the the

[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;
(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
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"



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