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Re: [Gmod-schema] [ISSUE] Load gff in chado
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From: RAJAONISON A. <mir...@ya...> - 2020-01-20 18:59:08
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Hi Scott,
Even with the --recreate_cache and --remove_lock, I still get the same error.
Miharimamy
(Re)creating the uniquename cache in the database...
Creating table...
Populating table...
Creating indexes...
Adjusting the primary key sequences (if necessary)...Done.
Preparing data for inserting into the chado database
(This may take a while ...)
Unable to find srcfeature NZ_CP027391.1 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4605, <GEN0> line 5939.
Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x25623e0)', 'Bio::SeqFeature::Annotated=HASH(0x2680c18)') called at chado-1.31/load/bin/gmod_bulk_load_gff3.pl line 851
Abnormal termination, trying to clean up...
Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...
Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting...
De : Scott Cain <sc...@sc...>
Envoyé : lundi 20 janvier 2020 20:56
À : RAJAONISON Andriamiharimamy <mir...@ya...>
Cc : GMOD Schema/Chado List <gmo...@li...>
Objet : Re: [Gmod-schema] [ISSUE] Load gff in chado
Hi Miharimamy,
Did you try running with the --recreate_cache option as suggested by the error message?
On Mon, Jan 20, 2020 at 6:54 AM RAJAONISON Andriamiharimamy <mir...@ya... <mailto:mir...@ya...> > wrote:
Hi Scott,
You were right, the issue lied in the line 2. The field separator was 4 spaces instead of tabulation.
I converted it and tried to load the file back but went back to the first error.
Thank you for your time,
Miharimamy
Preparing data for inserting into the chado database
(This may take a while ...)
Unable to find srcfeature NZ_CP027391.1 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4605, <GEN0> line 5939.
Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x297c120)', 'Bio::SeqFeature::Annotated=HASH(0x2bcd420)') called at chado-1.31/load/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> line 851
Abnormal termination, trying to clean up...
Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...
Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting...
##gff-version 3
NZ_CP027390.1 . chromosome 1 5901472 . . . ID=NZ_CP027390.1;Name=NZ_CP027390.1
NZ_CP027390.1 RefSeq gene 931 1197 . + . ID=gene0;Name=AX062_RS00010;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS00010
NZ_CP027390.1 RefSeq gene 1191 1577 . - . ID=gene1;Name=AX062_RS00015;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS00015
NZ_CP027390.1 RefSeq gene 10194 10736 . + . ID=gene10;Name=AX062_RS00060;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS00060
NZ_CP027390.1 RefSeq gene 80547 81860 . + . ID=gene100;Name=AX062_RS00510;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS00510
NZ_CP027390.1 RefSeq gene 918692 918997 . - . ID=gene1000;Name=AX062_RS05010;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS05010
NZ_CP027390.1 RefSeq gene 919105 919815 . + . ID=gene1001;Name=AX062_RS05015;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS05015
NZ_CP027390.1 RefSeq gene 919818 920378 . - . ID=gene1002;Name=AX062_RS05020;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS05020
NZ_CP027390.1 RefSeq gene 920413 920754 . - . ID=gene1003;Name=AX062_RS05025;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS05025
NZ_CP027390.1 RefSeq gene 920889 921215 . + . ID=gene1004;Name=AX062_RS05030;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS05030
NZ_CP027390.1 RefSeq gene 921252 921440 . + . ID=gene1005;Name=AX062_RS05035;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS05035
NZ_CP027390.1 RefSeq gene 921421 922635 . + . ID=gene1006;Name=AX062_RS05040;gbkey=Gene;gene_biotype=protein_coding;locus_tag=AX062_RS05040
De : Scott Cain <sc...@sc... <mailto:sc...@sc...> >
Envoyé : vendredi 17 janvier 2020 21:49
À : RAJAONISON Andriamiharimamy <mir...@ya... <mailto:mir...@ya...> >
Cc : GMOD Schema/Chado List <gmo...@li... <mailto:gmo...@li...> >
Objet : Re: [Gmod-schema] [ISSUE] Load gff in chado
Hi Miharimamy,
The end of the error message where it says "line 2" I'm pretty sure means the problem is in line 2 of your GFF file. Is that the line you added? What does it look like?
Scott
On Fri, Jan 17, 2020 at 5:57 AM RAJAONISON Andriamiharimamy <mir...@ya... <mailto:mir...@ya...> > wrote:
Hi Scott,
Thank you again for your help because adding the parent feature removes the srcfeature related error.
Yet I get another issue that I don’t understand :
--------------------- WARNING ---------------------
MSG: Can not set Bio::Location::Simple::end() equal to start; start not set
---------------------------------------------------
Use of uninitialized value $featuretype in pattern match (m//) at chado-1.31/load/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> line 819, <GEN0> line 2.
Use of uninitialized value $featuretype in pattern match (m//) at chado-1.31/load/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> line 820, <GEN0> line 2.
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: no cvterm for
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:447
STACK: Bio::GMOD::DB::Adapter::get_type /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm:4629
STACK: chado-1.31/load/bin/gmod_bulk_load_gff3.pl:848 <http://gmod_bulk_load_gff3.pl:848>
-----------------------------------------------------------
Abnormal termination, trying to clean up...
Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...
Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting...
Thank you
Miharimamy
De : Scott Cain <sc...@sc... <mailto:sc...@sc...> >
Envoyé : jeudi 16 janvier 2020 22:31
À : RAJAONISON Andriamiharimamy <mir...@ya... <mailto:mir...@ya...> >
Cc : GMOD Schema/Chado List <gmo...@li... <mailto:gmo...@li...> >
Objet : Re: [Gmod-schema] [ISSUE] Load gff in chado
Hi Miharimamy,
Thanks for sending this report. Generally, loading GFF into Chado can be difficult, as the perl-based loader that you are using can be quite particular about the format of the GFF and producers of GFF generally aren't so particular. Since the loader makes the (in my view, correct) decision to not load anything if it can't load everything in a file, it quits. So, taking each of the problems you found in order:
1. "dbxref=NCBI:" isn't a valid accession (presumably there should be something after the "NCBI:") and so the loader won't continue. Two options here are to contact SGD and point out that there is a problem with their GFF, or delete the offending item and try again, which it looks like you did for item 2.
2. If the item Note is missing from the cvterm table, I think that probably means that you didn't install the schema using the "make" procedure that would have installed some necessary items in the cv and cvterm table.
3 and 4: Messages that srcfeatures can't be found mean that the feature on which the features in your GFF reside hasn't been defined yet (that is, the thing referred to in column 1 of the GFF doesn't exist). Frequently, creators of GFF don't define the reference sequence in the GFF for whatever reason (it's not required by the GFF3 spec, since it might be credibly defined elsewhere). To define it in the GFF you have, add a line before anything else that looks something like this:
NZ_CP027390.1 . chromosome 1 1234566 . . . ID=NZ_CP027390.1;Name=NZ_CP027390.1
Where "NZ_CP027390.1" is the name of the reference sequence, "chromosome" is the Sequence Ontology term for the type of thing (other options would include "contig" and "supercontig"), and the "123456" is the length of the sequence.
Finally, I would add that using Chado through Tripal frequently makes life easier, though I think all of these issues would still have been problems (with the probable exception of item 2--Tripal would have initialized the "Note" item in cvterm I think).
Scott
On Thu, Jan 16, 2020 at 11:15 AM RAJAONISON Andriamiharimamy via Gmod-schema <gmo...@li... <mailto:gmo...@li...> > wrote:
Hi,
Hi,
Hope this mail will find you well. Send you my best wishes for this new year.
I am reaching to you because I have issues loading GFF files into you Chado. I tried several files but none of them seems to work.
Thank you in advance for you help
Miharimamy
1. The S.cerevisiae example in gmod.org <http://gmod.org>
Command :
chado-1.31/load/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> --organism yeast --gfffile saccharomyces/saccharomyces_cerevisiae.gff.sorted --fastafile saccharomyces/saccharomyces_cerevisiae.gff.sorted.fasta
Output :
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Error in line:
chrIII SGD chromosome 1 316620 . . . ID=chrIII;dbxref=NCBI:;Name=chrIII
Dbxref value 'NCBI:' did not conform to GFF3 specification
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:447
STACK: Bio::FeatureIO::gff::_handle_feature /usr/local/share/perl5/Bio/FeatureIO/gff.pm:659 <http://gff.pm:659>
STACK: Bio::FeatureIO::gff::next_feature /usr/local/share/perl5/Bio/FeatureIO/gff.pm:187 <http://gff.pm:187>
STACK: chado-1.31/load/bin/gmod_bulk_load_gff3.pl:782 <http://gmod_bulk_load_gff3.pl:782>
-----------------------------------------------------------
2. S.cerevisiae without dbxref
Command :
chado-1.31/load/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> --organism yeast --gfffile saccharomyces/test_saccharomyces_ncbi --fastafile saccharomyces/saccharomyces_cerevisiae.gff.sorted.fasta
Output :
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: I couldn't find the 'Note' cvterm in the database;
Did you load the feature property controlled vocabulary?
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:447
STACK: Bio::GMOD::DB::Adapter::handle_note /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm:3901
STACK: chado-1.31/load/bin/gmod_bulk_load_gff3.pl:974 <http://gmod_bulk_load_gff3.pl:974>
3. A GFF from NCBI
Command :
chado-1.31/load/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> --organism bacteria --gfffile GCF_000008865.2/GCF_003018035.1_ASM301803v1_genomic.gff.sorted
Output :
Unable to find srcfeature NZ_CP027390.1 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4605, <GEN0> line 2.
Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x241a8d0)', 'Bio::SeqFeature::Annotated=HASH(0x26c61d0)') called at chado-1.31/load/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> line 851
4. A GFF3 from prokka
Command :
chado-1.31/load/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> --organism bacteria -gfffile GFF3/GCF_000455285.gff.sorted --fastafile GFF3/GCF_000455285.gff.sorted.fasta
Output :
Unable to find srcfeature gnl|Prokka|GCF_000455285_1 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4605, <GEN0> line 2.
Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x33008f0)', 'Bio::SeqFeature::Annotated=HASH(0x35ac0a0)') called at chado-1.31/load/bin/gmod_bulk_load_gff3.pl <http://gmod_bulk_load_gff3.pl> line 851
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--
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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
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 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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