Fwd: gff3 file loading

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Fwd: gff3 file loading

Asma Riyaz

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






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Re: Fwd: gff3 file loading

Scott Cain
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Fwd: gff3 file loading

Asma Riyaz
Here is the full file.  

On Mon, Nov 24, 2014 at 3:25 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Fwd: gff3 file loading

Scott Cain
Hi Asma,

I don't see anything particularly wrong with this file that was cause the problem (it's possible that some of the underlying perl code has changed and the Chado software needs to be updated), BUT I also don't see any reason to sort this GFF anyway--the parents all come before the children, at least several hundred lines into the GFF file; I imagine it stays like that for the rest of the file.

Scott


On Mon, Nov 24, 2014 at 3:28 PM, Asma Riyaz <[hidden email]> wrote:
Here is the full file.  

On Mon, Nov 24, 2014 at 3:25 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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Re: Fwd: gff3 file loading

Asma Riyaz
I am using Chado 1.23, is this not updated version of Chado?

On Mon, Nov 24, 2014 at 3:38 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I don't see anything particularly wrong with this file that was cause the problem (it's possible that some of the underlying perl code has changed and the Chado software needs to be updated), BUT I also don't see any reason to sort this GFF anyway--the parents all come before the children, at least several hundred lines into the GFF file; I imagine it stays like that for the rest of the file.

Scott


On Mon, Nov 24, 2014 at 3:28 PM, Asma Riyaz <[hidden email]> wrote:
Here is the full file.  

On Mon, Nov 24, 2014 at 3:25 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
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Re: Fwd: gff3 file loading

Scott Cain
No, it is the current release, but it is also two years old.  Some underlying perl module that I don't control may have changed, causing the sorting script to break, but since you don't need it, I'd suggest that you not worry about it for the moment.


On Mon, Nov 24, 2014 at 4:47 PM, Asma Riyaz <[hidden email]> wrote:
I am using Chado 1.23, is this not updated version of Chado?

On Mon, Nov 24, 2014 at 3:38 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I don't see anything particularly wrong with this file that was cause the problem (it's possible that some of the underlying perl code has changed and the Chado software needs to be updated), BUT I also don't see any reason to sort this GFF anyway--the parents all come before the children, at least several hundred lines into the GFF file; I imagine it stays like that for the rest of the file.

Scott


On Mon, Nov 24, 2014 at 3:28 PM, Asma Riyaz <[hidden email]> wrote:
Here is the full file.  

On Mon, Nov 24, 2014 at 3:25 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Get technology previously reserved for billion-dollar corporations, FREE
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Re: Fwd: gff3 file loading

Asma Riyaz
So according to you if the script is breaking, its because the gff3 file I sent you earlier has not been sorted properly?

On Mon, Nov 24, 2014 at 5:01 PM, Scott Cain <[hidden email]> wrote:
No, it is the current release, but it is also two years old.  Some underlying perl module that I don't control may have changed, causing the sorting script to break, but since you don't need it, I'd suggest that you not worry about it for the moment.


On Mon, Nov 24, 2014 at 4:47 PM, Asma Riyaz <[hidden email]> wrote:
I am using Chado 1.23, is this not updated version of Chado?

On Mon, Nov 24, 2014 at 3:38 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I don't see anything particularly wrong with this file that was cause the problem (it's possible that some of the underlying perl code has changed and the Chado software needs to be updated), BUT I also don't see any reason to sort this GFF anyway--the parents all come before the children, at least several hundred lines into the GFF file; I imagine it stays like that for the rest of the file.

Scott


On Mon, Nov 24, 2014 at 3:28 PM, Asma Riyaz <[hidden email]> wrote:
Here is the full file.  

On Mon, Nov 24, 2014 at 3:25 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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Re: Fwd: gff3 file loading

Scott Cain
Hi Asma,

No, sorry--I may have assumed too much; I thought you were running the gff preprocessing script (whose man function is to sort and split gff files), and I pointed out that it doesn't need sorting.  Exactly what command were you running when you got that error message?

Scott


On Mon, Nov 24, 2014 at 5:05 PM, Asma Riyaz <[hidden email]> wrote:
So according to you if the script is breaking, its because the gff3 file I sent you earlier has not been sorted properly?

On Mon, Nov 24, 2014 at 5:01 PM, Scott Cain <[hidden email]> wrote:
No, it is the current release, but it is also two years old.  Some underlying perl module that I don't control may have changed, causing the sorting script to break, but since you don't need it, I'd suggest that you not worry about it for the moment.


On Mon, Nov 24, 2014 at 4:47 PM, Asma Riyaz <[hidden email]> wrote:
I am using Chado 1.23, is this not updated version of Chado?

On Mon, Nov 24, 2014 at 3:38 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I don't see anything particularly wrong with this file that was cause the problem (it's possible that some of the underlying perl code has changed and the Chado software needs to be updated), BUT I also don't see any reason to sort this GFF anyway--the parents all come before the children, at least several hundred lines into the GFF file; I imagine it stays like that for the rest of the file.

Scott


On Mon, Nov 24, 2014 at 3:28 PM, Asma Riyaz <[hidden email]> wrote:
Here is the full file.  

On Mon, Nov 24, 2014 at 3:25 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Fwd: gff3 file loading

Asma Riyaz
gmod_gff3_preprocessor.pl --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
(I only substituted the filenames)

On Mon, Nov 24, 2014 at 5:10 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

No, sorry--I may have assumed too much; I thought you were running the gff preprocessing script (whose man function is to sort and split gff files), and I pointed out that it doesn't need sorting.  Exactly what command were you running when you got that error message?

Scott


On Mon, Nov 24, 2014 at 5:05 PM, Asma Riyaz <[hidden email]> wrote:
So according to you if the script is breaking, its because the gff3 file I sent you earlier has not been sorted properly?

On Mon, Nov 24, 2014 at 5:01 PM, Scott Cain <[hidden email]> wrote:
No, it is the current release, but it is also two years old.  Some underlying perl module that I don't control may have changed, causing the sorting script to break, but since you don't need it, I'd suggest that you not worry about it for the moment.


On Mon, Nov 24, 2014 at 4:47 PM, Asma Riyaz <[hidden email]> wrote:
I am using Chado 1.23, is this not updated version of Chado?

On Mon, Nov 24, 2014 at 3:38 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I don't see anything particularly wrong with this file that was cause the problem (it's possible that some of the underlying perl code has changed and the Chado software needs to be updated), BUT I also don't see any reason to sort this GFF anyway--the parents all come before the children, at least several hundred lines into the GFF file; I imagine it stays like that for the rest of the file.

Scott


On Mon, Nov 24, 2014 at 3:28 PM, Asma Riyaz <[hidden email]> wrote:
Here is the full file.  

On Mon, Nov 24, 2014 at 3:25 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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Re: Fwd: gff3 file loading

Scott Cain
Right--your GFF doesn't need preprocessing, so don't worry about it.



On Mon, Nov 24, 2014 at 5:12 PM, Asma Riyaz <[hidden email]> wrote:
gmod_gff3_preprocessor.pl --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
(I only substituted the filenames)

On Mon, Nov 24, 2014 at 5:10 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

No, sorry--I may have assumed too much; I thought you were running the gff preprocessing script (whose man function is to sort and split gff files), and I pointed out that it doesn't need sorting.  Exactly what command were you running when you got that error message?

Scott


On Mon, Nov 24, 2014 at 5:05 PM, Asma Riyaz <[hidden email]> wrote:
So according to you if the script is breaking, its because the gff3 file I sent you earlier has not been sorted properly?

On Mon, Nov 24, 2014 at 5:01 PM, Scott Cain <[hidden email]> wrote:
No, it is the current release, but it is also two years old.  Some underlying perl module that I don't control may have changed, causing the sorting script to break, but since you don't need it, I'd suggest that you not worry about it for the moment.


On Mon, Nov 24, 2014 at 4:47 PM, Asma Riyaz <[hidden email]> wrote:
I am using Chado 1.23, is this not updated version of Chado?

On Mon, Nov 24, 2014 at 3:38 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I don't see anything particularly wrong with this file that was cause the problem (it's possible that some of the underlying perl code has changed and the Chado software needs to be updated), BUT I also don't see any reason to sort this GFF anyway--the parents all come before the children, at least several hundred lines into the GFF file; I imagine it stays like that for the rest of the file.

Scott


On Mon, Nov 24, 2014 at 3:28 PM, Asma Riyaz <[hidden email]> wrote:
Here is the full file.  

On Mon, Nov 24, 2014 at 3:25 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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Re: Fwd: gff3 file loading

Asma Riyaz

Here is the command that I am running:

gmod_bulk_load_gff3.pl --organism Tribolium castaneum --gfffile /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 

end up in:

DBD::Pg::st fetchrow_array failed: no statement executing at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 1209, <GEN0> line 2.

Tribolium organism not found in the database at /usr/local/bin/gmod_bulk_load_gff3.pl line 752, <GEN0> line 2.


Abnormal termination, trying to clean up...


Trying to remove the run lock (so that --remove_lock won't be needed)...

Exiting...

I have checked the chado database:

chado1=# select * from organism;

 organism_id | abbreviation |   genus   |  species  | common_name  |   comment    

-------------+--------------+-----------+-----------+--------------+--------------

          17 | T. Castaneum | Tribolium | Castaneum | T. Castaneum | T. Castaneum

(1 row)

Here is .gmodrc

export GMOD_ROOT='/usr/local/gmod'

export CHADO_DB_NAME='chado1'


Where am I going wrong this time around?

Asma






On Mon, Nov 24, 2014 at 6:11 PM, Scott Cain <[hidden email]> wrote:
Right--your GFF doesn't need preprocessing, so don't worry about it.



On Mon, Nov 24, 2014 at 5:12 PM, Asma Riyaz <[hidden email]> wrote:
gmod_gff3_preprocessor.pl --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
(I only substituted the filenames)

On Mon, Nov 24, 2014 at 5:10 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

No, sorry--I may have assumed too much; I thought you were running the gff preprocessing script (whose man function is to sort and split gff files), and I pointed out that it doesn't need sorting.  Exactly what command were you running when you got that error message?

Scott


On Mon, Nov 24, 2014 at 5:05 PM, Asma Riyaz <[hidden email]> wrote:
So according to you if the script is breaking, its because the gff3 file I sent you earlier has not been sorted properly?

On Mon, Nov 24, 2014 at 5:01 PM, Scott Cain <[hidden email]> wrote:
No, it is the current release, but it is also two years old.  Some underlying perl module that I don't control may have changed, causing the sorting script to break, but since you don't need it, I'd suggest that you not worry about it for the moment.


On Mon, Nov 24, 2014 at 4:47 PM, Asma Riyaz <[hidden email]> wrote:
I am using Chado 1.23, is this not updated version of Chado?

On Mon, Nov 24, 2014 at 3:38 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I don't see anything particularly wrong with this file that was cause the problem (it's possible that some of the underlying perl code has changed and the Chado software needs to be updated), BUT I also don't see any reason to sort this GFF anyway--the parents all come before the children, at least several hundred lines into the GFF file; I imagine it stays like that for the rest of the file.

Scott


On Mon, Nov 24, 2014 at 3:28 PM, Asma Riyaz <[hidden email]> wrote:
Here is the full file.  

On Mon, Nov 24, 2014 at 3:25 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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Re: Fwd: gff3 file loading

Scott Cain
Hi Asma,

You need double quotes around the genus and species; without them, Linux thinks the only argument for the organism flag is the first word. 


Sent from my iPad

On Nov 24, 2014, at 7:31 PM, Asma Riyaz <[hidden email]> wrote:

Here is the command that I am running:

gmod_bulk_load_gff3.pl --organism Tribolium castaneum --gfffile /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 

end up in:

DBD::Pg::st fetchrow_array failed: no statement executing at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 1209, <GEN0> line 2.

Tribolium organism not found in the database at /usr/local/bin/gmod_bulk_load_gff3.pl line 752, <GEN0> line 2.


Abnormal termination, trying to clean up...


Trying to remove the run lock (so that --remove_lock won't be needed)...

Exiting...

I have checked the chado database:

chado1=# select * from organism;

 organism_id | abbreviation |   genus   |  species  | common_name  |   comment    

-------------+--------------+-----------+-----------+--------------+--------------

          17 | T. Castaneum | Tribolium | Castaneum | T. Castaneum | T. Castaneum

(1 row)

Here is .gmodrc

export GMOD_ROOT='/usr/local/gmod'

export CHADO_DB_NAME='chado1'


Where am I going wrong this time around?

Asma






On Mon, Nov 24, 2014 at 6:11 PM, Scott Cain <[hidden email]> wrote:
Right--your GFF doesn't need preprocessing, so don't worry about it.



On Mon, Nov 24, 2014 at 5:12 PM, Asma Riyaz <[hidden email]> wrote:
gmod_gff3_preprocessor.pl --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
(I only substituted the filenames)

On Mon, Nov 24, 2014 at 5:10 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

No, sorry--I may have assumed too much; I thought you were running the gff preprocessing script (whose man function is to sort and split gff files), and I pointed out that it doesn't need sorting.  Exactly what command were you running when you got that error message?

Scott


On Mon, Nov 24, 2014 at 5:05 PM, Asma Riyaz <[hidden email]> wrote:
So according to you if the script is breaking, its because the gff3 file I sent you earlier has not been sorted properly?

On Mon, Nov 24, 2014 at 5:01 PM, Scott Cain <[hidden email]> wrote:
No, it is the current release, but it is also two years old.  Some underlying perl module that I don't control may have changed, causing the sorting script to break, but since you don't need it, I'd suggest that you not worry about it for the moment.


On Mon, Nov 24, 2014 at 4:47 PM, Asma Riyaz <[hidden email]> wrote:
I am using Chado 1.23, is this not updated version of Chado?

On Mon, Nov 24, 2014 at 3:38 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I don't see anything particularly wrong with this file that was cause the problem (it's possible that some of the underlying perl code has changed and the Chado software needs to be updated), BUT I also don't see any reason to sort this GFF anyway--the parents all come before the children, at least several hundred lines into the GFF file; I imagine it stays like that for the rest of the file.

Scott


On Mon, Nov 24, 2014 at 3:28 PM, Asma Riyaz <[hidden email]> wrote:
Here is the full file.  

On Mon, Nov 24, 2014 at 3:25 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Can you please send a sample of the GFF that caused the problem (or the whole file if it's not too big)?  If you send a sample, please make sure it includes many lines around the one that it says is probably the problem.

Scott


On Mon, Nov 24, 2014 at 2:54 PM, Asma Riyaz <[hidden email]> wrote:

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Nov 24, 2014 at 2:36 PM
Subject: gff3 file loading
To: gmod-gbrowse <[hidden email]>, Scott Cain <[hidden email]>


Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma






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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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