[Bioperl-l] FW: bp_genbank2gff3- Unflattening error
Jayaraman, Pushkala
pjayaraman at mcw.edu
Thu Oct 7 20:46:19 UTC 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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