[Bioperl-l] Problem with bp_pg_bulk_load_gff

[Scott Cain]

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