[Bioperl-l] Problem with bp_pg_bulk_load_gff

[Marco Blanchette]

Many tx Scott--

I created the environment variable $TMPDIR pointing to a directory in my
home by:

export TMPDIR=$HOME/Library/tmp

I included that line in my .bash_profile

Now when I run:
$ bp_pg_bulk_load_gff.pl -d chr4 -c dmel-4-r4.2.1.gff

Everything is perfect

Many thanks

Marco


On 3/1/06 7:26 PM, "Scott Cain" <cain at cshl.edu> wrote:

> 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 what¹s 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
>> -- 
>> 


Marco Blanchette, Ph.D.

mblanche at 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