ERROR: value is out of range for type integer

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ERROR: value is out of range for type integer

Francisco García Atienza
Hi,

I'm trying to load a gff3 file to Chado with the following command:

$ gmod_bulk_load_gff3.pl --organism 'Picea abies' --dbname webapollochado_spruce -g index.gff3

but my problem is that the organism has too many features and the 'seqlen' value is out of range for an integer:

Loading data into feature table ...
DBD::Pg::db pg_endcopy failed: ERROR:  value "-2147489583" is out of range for type integer.

My gff3 file looks like this (index.gff3):

MA_1 spruce chromosome 16 89935 . . . ID=MA_1;Name=MA_1
MA_2 spruce chromosome 91092 35142 . . . ID=MA_2;Name=MA_2
MA_3 spruce chromosome 126690 30536 . . . ID=MA_3;Name=MA_3
MA_4 spruce chromosome 157624 53646 . . . ID=MA_4;Name=MA_4
MA_5 spruce chromosome 211957 87820 . . . ID=MA_5;Name=MA_5
MA_7 spruce chromosome 300891 53329 . . . ID=MA_7;Name=MA_7
MA_10 spruce chromosome 354904 54367 . . . ID=MA_10;Name=MA_10
MA_11 spruce chromosome 409968 43614 . . . ID=MA_11;Name=MA_11
MA_12 spruce chromosome 454145 27891 . . . ID=MA_12;Name=MA_12
MA_13 spruce chromosome 482402 45192 . . . ID=MA_13;Name=MA_13

.
.
.

MA_10437271 spruce chromosome 3847179253 23554 . . . ID=MA_10437271;Name=MA_10437271
MA_10437272 spruce chromosome 3847203125 36276 . . . ID=MA_10437272;Name=MA_10437272
MA_10437273 spruce chromosome 3847239878 17773 . . . ID=MA_10437273;Name=MA_10437273
MA_10437274 spruce chromosome 3847257897 20420 . . . ID=MA_10437274;Name=MA_10437274
MA_10437275 spruce chromosome 3847278596 24448 . . . ID=MA_10437275;Name=MA_10437275
MA_10437276 spruce chromosome 3847303373 58239 . . . ID=MA_10437276;Name=MA_10437276
MA_10437277 spruce chromosome 3847362363 35232 . . . ID=MA_10437277;Name=MA_10437277
MA_10437278 spruce chromosome 3847398082 69798 . . . ID=MA_10437278;Name=MA_10437278
MA_10437279 spruce chromosome 3847468776 78691 . . . ID=MA_10437279;Name=MA_10437279
MA_10437280 spruce chromosome 3847548474 43457 . . . ID=MA_10437280;Name=MA_10437280


What can I do? Is it possible to change the type without any problems? 

Thank you.

Best.

/Francisco.













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Re: ERROR: value is out of range for type integer

Scott Cain
Hi Francisco,

There are a few problems.  First, the GFF3 spec specifies that the start coordinate is less than or equal to the end coordinate. The reason there is a large negative number in that error message is that it's calculating the length of a sequence and getting that because the start coordinate is larger than he end coordinate. 

Next, are these features really chromosomes (or more likely, contigs since you have 10 million of them)?  If so, the start coordinate should always be 1 and the end coordinate should be the length of the sequence. If they're some other type of feature, then you need to fix more than just the coordinates: the type needs to be changed to whatever type of thing they are and the name of the reference sequence needs to be changed to whatever the name of the chromosome it's on, so it would look something like this:

Chr1 spruce type  54367 354904 . . . Name=MA_10

You don't need IDs if the feature isn't being referred to by anything else. 

Finally, there still might be a problem after theses things are fixed: I know that big trees have big genomes.  If an individual spruce chromosome is bigger than 2 Gb, the length might be too large to store in the seqlen field.  If that's the case, we'll have to alter the structure of the database slightly. 

Scott


Sent from my iPad

On Feb 11, 2014, at 8:29 AM, Francisco García Atienza <[hidden email]> wrote:

Hi,

I'm trying to load a gff3 file to Chado with the following command:

$ gmod_bulk_load_gff3.pl --organism 'Picea abies' --dbname webapollochado_spruce -g index.gff3

but my problem is that the organism has too many features and the 'seqlen' value is out of range for an integer:

Loading data into feature table ...
DBD::Pg::db pg_endcopy failed: ERROR:  value "-2147489583" is out of range for type integer.

My gff3 file looks like this (index.gff3):

MA_1 spruce chromosome 16 89935 . . . ID=MA_1;Name=MA_1
MA_2 spruce chromosome 91092 35142 . . . ID=MA_2;Name=MA_2
MA_3 spruce chromosome 126690 30536 . . . ID=MA_3;Name=MA_3
MA_4 spruce chromosome 157624 53646 . . . ID=MA_4;Name=MA_4
MA_5 spruce chromosome 211957 87820 . . . ID=MA_5;Name=MA_5
MA_7 spruce chromosome 300891 53329 . . . ID=MA_7;Name=MA_7
MA_10 spruce chromosome 354904 54367 . . . ID=MA_10;Name=MA_10
MA_11 spruce chromosome 409968 43614 . . . ID=MA_11;Name=MA_11
MA_12 spruce chromosome 454145 27891 . . . ID=MA_12;Name=MA_12
MA_13 spruce chromosome 482402 45192 . . . ID=MA_13;Name=MA_13

.
.
.

MA_10437271 spruce chromosome 3847179253 23554 . . . ID=MA_10437271;Name=MA_10437271
MA_10437272 spruce chromosome 3847203125 36276 . . . ID=MA_10437272;Name=MA_10437272
MA_10437273 spruce chromosome 3847239878 17773 . . . ID=MA_10437273;Name=MA_10437273
MA_10437274 spruce chromosome 3847257897 20420 . . . ID=MA_10437274;Name=MA_10437274
MA_10437275 spruce chromosome 3847278596 24448 . . . ID=MA_10437275;Name=MA_10437275
MA_10437276 spruce chromosome 3847303373 58239 . . . ID=MA_10437276;Name=MA_10437276
MA_10437277 spruce chromosome 3847362363 35232 . . . ID=MA_10437277;Name=MA_10437277
MA_10437278 spruce chromosome 3847398082 69798 . . . ID=MA_10437278;Name=MA_10437278
MA_10437279 spruce chromosome 3847468776 78691 . . . ID=MA_10437279;Name=MA_10437279
MA_10437280 spruce chromosome 3847548474 43457 . . . ID=MA_10437280;Name=MA_10437280


What can I do? Is it possible to change the type without any problems? 

Thank you.

Best.

/Francisco.












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Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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