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Re: [Gmod-schema] [ISSUE] Load gff in chado
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From: Scott C. <sc...@sc...> - 2020-01-20 18:21:41
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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...> 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 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...>
> *Envoyé :* vendredi 17 janvier 2020 21:49
> *À :* RAJAONISON Andriamiharimamy <mir...@ya...>
> *Cc :* GMOD Schema/Chado List <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...> 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 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 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
>
> -----------------------------------------------------------
>
>
>
> 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...>
> *Envoyé :* jeudi 16 janvier 2020 22:31
> *À :* RAJAONISON Andriamiharimamy <mir...@ya...>
> *Cc :* GMOD Schema/Chado List <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...> 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
>
> *Command : *
>
> chado-1.31/load/bin/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
>
> STACK: Bio::FeatureIO::gff::next_feature
> /usr/local/share/perl5/Bio/FeatureIO/gff.pm:187
>
> STACK: chado-1.31/load/bin/gmod_bulk_load_gff3.pl:782
>
> -----------------------------------------------------------
>
> 1. S.cerevisiae without dbxref
>
> *Command : *
>
> chado-1.31/load/bin/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
>
>
>
> 1. A GFF from NCBI
>
> *Command : *
>
> chado-1.31/load/bin/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 line 851
>
>
>
> 1. A GFF3 from prokka
>
> *Command :*
>
> chado-1.31/load/bin/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 line 851
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
>
> --
>
> ------------------------------------------------------------------------
> 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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