[Bioperl-l] Problem with bp_pg_bulk_load_gff

Scott Cain cain at cshl.edu
Thu Mar 2 03:26:45 UTC 2006


Hi Marco,

Please always send questions about bioperl to both the bioperl list and
the author so that the questions (and answers) can be archived.

The Postgres bulk loader tries to use a temporary directory to write
files to; it tries to use these directories in order:

  $TMPDIR (environment variables)
  $TMP
  /usr/tmp

So if you don't have either TMPDIR or TMP environment variables set, it
will try to use /usr/tmp.  So, to fix this, either set one of those
variables, or create /usr/tmp and make it world readable and writable.

Scott


On Wed, 2006-03-01 at 16:23 -0800, Marco Blanchette wrote:
> Scott--
> 
> I am trying to use the pg_bulk_load_gff.pl script you wrote without
> any success. I have PostgreSQL up and running and I can use:
> $ bp_load_gff.pl --adaptor dbi::pg  -d chr4  --create
> dmel-4-r4.2.1.gff
> to load a gff file to the chr4 PostgresSQL database.
> 
> Here is the output I get when I run your script:
> 
> $ bp_pg_bulk_load_gff.pl -d chr4 dmel-4-r4.2.1.gff 
>         
> This operation will delete all existing data in database chr4.
>  Continue? y
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "pk_fdna" for table "fdna"
> NOTICE:  CREATE TABLE will create implicit sequence "fdata_fid_seq"
> for serial column "fdata.fid"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "pk_fdata" for table "fdata"
> NOTICE:  CREATE TABLE will create implicit sequence
> "fattribute_fattribute_id_seq" for serial column
> "fattribute.fattribute_id"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "pk_fattribute" for table "fattribute"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "pk_fmeta" for table "fmeta"
> NOTICE:  CREATE TABLE will create implicit sequence
> "ftype_ftypeid_seq" for serial column "ftype.ftypeid"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "pk_ftype" for table "ftype"
> NOTICE:  CREATE TABLE / UNIQUE will create implicit index
> "ftype_ftype" for table "ftype"
> NOTICE:  CREATE TABLE will create implicit sequence "fgroup_gid_seq"
> for serial column "fgroup.gid"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "pk_fgroup" for table "fgroup"
> fdata: No such file or directory at /usr/bin/bp_pg_bulk_load_gff.pl
> line 213.
> 
> Somehow it breaks at line 213 within the foreach block:
> 
> 212 foreach (@files) {
> 213   $FH{$_} = IO::File->new("$tmpdir/$_.$$",">") or die $_,": $!";
> 214   $FH{$_}->autoflush;
> 215 }
> 
> Any idea what’s the problem??
> 
> Many tx
> 
> Marco
> ______________________________
> Marco Blanchette, Ph.D.
> 
> mblanche at uclink.berkeley.edu
> 
> Donald C. Rio's lab
> Department of Molecular and Cell Biology
> 16 Barker Hall
> University of California
> Berkeley, CA 94720-3204
> 
> Tel: (510) 642-1084
> Cell: (510) 847-0996
> Fax: (510) 642-6062
> -- 
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory




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