[Bioperl-l] FW: bp_genbank2gff3- Unflattening error

Jayaraman, Pushkala pjayaraman at mcw.edu
Thu Oct 7 16:46:19 EDT 2010


I apologize, 

I should have sent it to the forum first.. 

 

 

FYI.. 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala 
Sent: Thursday, October 07, 2010 3:07 PM
To: 'cjm at fruitfly.org'
Subject: bp_genbank2gff3- Unflattening error

 

Hi Chris, 

I saw your response in a  post about Unflattener.pm here;

http://generic-model-organism-system-database.450254.n5.nabble.com/genba
nk-to-gff3-conversion-problem-td460065.html

 

hence decided to fwd this to you.. 

I have no clue what is going on.. 

 

NT_010799 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: PROBLEM, SEVERITY==1

Container feature does not spatially contain subfeature. Perhaps this is
a dicistronic gene? I am expanding the parent feature

SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14

 

SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine
(C-C motif) ligand 14 (CCL14), transcript variant 1

 

STACK Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:952

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:2170

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1798

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1503

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

 

 

 

 

 

I even get another error under Unflattener.pm in another region.. this
is how it is described:

 

PROBLEM:

NT_024524 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: 1 there is a conflict with exons; there was an explicitly stated
exon with location 22748456..22748502, yet I cannot generate this exon
from the supplied mRNA locations

 

1 There are some inferred exons that are not in the explicit exon list;
they are the exons at locations:

10982777..10983033

9516278..9517506

1225346..1225429

33491613..33491816

58797942..58798087

7323184..7323367

21253638..21253755

59172140..59172196

54309290..54310329

8988942..8989171

26569087..26569218

6479986..6480032

32266760..32267377

.....

 

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1631

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

-------------------------------------

 

 

I do not know what is going on.. is it something that the data has or
something that I am doing wrong? 

the section of the genbank file that gives out this error is pasted
below.. 

 

 

 

 

Please help,

 

 

 

 

 

gene            complement(9047672..9065992)

                     /gene="CCL14-CCL15"

                     /note="chemokine ligand 14, chemokine ligand 15

                     transcription unit"

                     /db_xref="GeneID:348249"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004166.3"

                     /db_xref="GI:34335177"

                     /db_xref="GeneID:6358"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032964.2"

                     /db_xref="GI:34335178"

                     /db_xref="GeneID:6359"

                     /db_xref="MIM:601393"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032962.2"

                     /db_xref="GI:34335175"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004167.3"

                     /db_xref="GI:34335181"

                     /db_xref="GeneID:6359"

                     /db_xref="HGNC:10613"

                     /db_xref="MIM:601393"

     gene            complement(9047672..9050719)

                     /gene="CCL14"

                     /note="chemokine (C-C motif) ligand 14; synonyms:
CC-1,

                     CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
SCYL2,

                     SCYA14"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050719))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 3"

                     /transcript_id="NM_032963.2"

                     /db_xref="GI:34335176"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     STS             9047707..9047892

                     /standard_name="STS-H22017"

                     /db_xref="UniSTS:13833"

     STS             9047767..9047885

                     /standard_name="GDB:607751"

                     /db_xref="UniSTS:158278"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_116739.1"

                     /db_xref="GI:14589961"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_004157.1"

                     /db_xref="GI:4759070"

                     /db_xref="CCDS:CCDS32624.1"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 2

                     precursor"

                     /protein_id="NP_116738.1"

                     /db_xref="GI:14589959"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:pjayaraman at mcw.edu] 
Sent: Thursday, October 07, 2010 2:56 PM
To: gmod-devel at lists.sourceforge.net
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: [Gmod-gbrowse] FW: bp_genbank2gff3- Unflattening error

 

I am providing the section of the genbank file here as I am not able to
attach the entire genbank file here(duh!):

 

     gene            complement(9047672..9065992)

                     /gene="CCL14-CCL15"

                     /note="chemokine ligand 14, chemokine ligand 15

                     transcription unit"

                     /db_xref="GeneID:348249"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004166.3"

                     /db_xref="GI:34335177"

                     /db_xref="GeneID:6358"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050720,9061737..9061876,9062296..9062407,

                     9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 1"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032964.2"

                     /db_xref="GI:34335178"

                     /db_xref="GeneID:6359"

                     /db_xref="MIM:601393"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_032962.2"

                     /db_xref="GI:34335175"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050720,9061737..9061876,

 
9062296..9062407,9062882..9062941,9065436..9065992))

                     /gene="CCL15"

                     /product="chemokine (C-C motif) ligand 15 (CCL15),

                     transcript variant 2"

                     /exception="unclassified transcription discrepancy"

                     /transcript_id="NM_004167.3"

                     /db_xref="GI:34335181"

                     /db_xref="GeneID:6359"

                     /db_xref="HGNC:10613"

                     /db_xref="MIM:601393"

     gene            complement(9047672..9050719)

                     /gene="CCL14"

                     /note="chemokine (C-C motif) ligand 14; synonyms:
CC-1,

                     CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
SCYL2,

                     SCYA14"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     mRNA            complement(join(9047672..9047904,9048354..9048468,

                     9050587..9050719))

                     /gene="CCL14"

                     /product="chemokine (C-C motif) ligand 14 (CCL14),

                     transcript variant 3"

                     /transcript_id="NM_032963.2"

                     /db_xref="GI:34335176"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     STS             9047707..9047892

                     /standard_name="STS-H22017"

                     /db_xref="UniSTS:13833"

     STS             9047767..9047885

                     /standard_name="GDB:607751"

                     /db_xref="UniSTS:158278"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_116739.1"

                     /db_xref="GI:14589961"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 1

                     precursor"

                     /protein_id="NP_004157.1"

                     /db_xref="GI:4759070"

                     /db_xref="CCDS:CCDS32624.1"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

     CDS             complement(join(9047817..9047904,9048354..9048468,

                     9049764..9049811,9050587..9050665))

                     /gene="CCL14"

                     /note="small inducible cytokine subfamily A
(Cys-Cys),

                     member 14; chemokine CC-1; chemokine CC-3"

                     /codon_start=1

                     /product="chemokine (C-C motif) ligand 14 isoform 2

                     precursor"

                     /protein_id="NP_116738.1"

                     /db_xref="GI:14589959"

                     /db_xref="GeneID:6358"

                     /db_xref="HGNC:10612"

                     /db_xref="MIM:601392"

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala 
Sent: Thursday, October 07, 2010 2:43 PM
To: gmod-gbrowse at lists.sourceforge.net
Subject: bp_genbank2gff3- Unflattening error

 

Hello, 

Running the bp_genbank2gff3.pm gives me:

 

NT_010799 Unflattening error:

Details: 

------------- EXCEPTION -------------

MSG: PROBLEM, SEVERITY==1

Container feature does not spatially contain subfeature. Perhaps this is
a dicistronic gene? I am expanding the parent feature

SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14

 

SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine
(C-C motif) ligand 14 (CCL14), transcript variant 1

 

STACK Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:952

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:2170

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1798

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattene
r.pm:1503

STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915

STACK main::unflatten_seq
/usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914

STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411

 

 

 

Ive never seen this error before and have no clue how to resolve this as
the input is a .gbk file and the script is a BIOPerl script.  Because we
seem to be losing a  lot of gene information in a particular contig. 

Am I doing anything wrong?

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

 

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