[Artemis-users] cannot open a gff3 file "RANGE NOT FOUND"

Sat, 30 Jan 2016 07:49:44 -0800 

Hello,
I cannot open a gene gff3 file in Artemis corresponding to scaffold_0001 that you will find at the following link https://filesender-beta.renater.fr/?s=download&token=fce5e89a-76af-e9aa-c92c-fc410edb1f27
In the artemis log window the message that I have is "RANGE NOT FOUND" but if I select the base range 14497441..14497494 for instance it is found. Also the first gene of the gff3 file that I copy paste in a test file here enclosed loads correctly in artemis.
I tried this gff3 validator with success http://genometools.org/cgi-bin/gff3validator.cgi 

Have you an idea of what is wrong with my full gff3 file ?


Thank you very much, best regards,

30 janv. 16:10:08 - 1.6.0_65
30 janv. 16:10:08 - Apple Inc.
30 janv. 16:10:08 - /Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home 
30 janv. 16:10:08 - Mac OS X
30 janv. 16:10:08 - Max. Heap Memory / Mb: 530
30 janv. 16:10:08 - Starting application: Artemis
30 janv. 16:10:08 - Diana.ini not found
30 janv. 16:10:08 - options not found
30 janv. 16:10:08 - options.txt not found
30 janv. 16:10:08 - options.text not found
30 janv. 16:10:08 - /Users/SIDIBEBOCS/.artemis_options not found
30 janv. 16:10:08 - os.name mac os x
30 janv. 16:10:14 - Working directory: /Applications/Artemis
30 janv. 16:15:14 - BAM & VCF not visible
while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: gene can't have locus_tag as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: gene can't have gbkey as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: gene can't have gene as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: mRNA can't have exception as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: mRNA can't have transcript_id as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: exon can't have product as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: polypeptide can't have codon_start as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: ncRNA can't have ncrna_class as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: gene can't have pseudo as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: gene can't have start_range as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: gene can't have partial as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: gene can't have end_range as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: tRNA can't have anticodon as a qualifier while reading from EUCGR-NCBI100-sequence_feature-locus_tag-genfam-scaffold0001.gff3: tRNA can't have part as a qualifier 
30 janv. 16:15:49 - RANGE NOT FOUND 14497441..14497494
30 janv. 16:15:49 - RANGE NOT FOUND 14491236..14493407
30 janv. 16:15:49 - RANGE NOT FOUND 14491236..14493407
30 janv. 16:15:49 - RANGE NOT FOUND 14474887..14474955
30 janv. 16:15:49 - RANGE NOT FOUND 14476836..14476949
30 janv. 16:15:49 - RANGE NOT FOUND 14456459..14459782
30 janv. 16:15:49 - RANGE NOT FOUND 14456459..14459782
30 janv. 16:15:49 - RANGE NOT FOUND 14383036..14383224
30 janv. 16:15:49 - RANGE NOT FOUND 14356897..14357019
30 janv. 16:15:49 - RANGE NOT FOUND 14351666..14351699
30 janv. 16:15:49 - RANGE NOT FOUND 38518241..38518599
30 janv. 16:15:49 - RANGE NOT FOUND 38518241..38518599
30 janv. 16:15:49 - RANGE NOT FOUND 38514214..38514259
30 janv. 16:15:49 - RANGE NOT FOUND 38503281..38503410
30 janv. 16:15:49 - RANGE NOT FOUND 38497748..38497955
30 janv. 16:15:49 - RANGE NOT FOUND 38485273..38485459
30 janv. 16:15:49 - RANGE NOT FOUND 38462568..38462946
30 janv. 16:15:49 - RANGE NOT FOUND 38462568..38462946
30 janv. 16:15:49 - RANGE NOT FOUND 38462568..38462949
30 janv. 16:15:49 - RANGE NOT FOUND 38462568..38462949
30 janv. 16:15:49 - RANGE NOT FOUND 38455814..38455960
30 janv. 16:15:49 - RANGE NOT FOUND 38449482..38449682
30 janv. 16:15:49 - RANGE NOT FOUND 38441453..38441671
30 janv. 16:15:49 - RANGE NOT FOUND 14288500..14288533
30 janv. 16:15:49 - RANGE NOT FOUND 14260954..14261828
30 janv. 16:15:49 - RANGE NOT FOUND 14253463..14254326
30 janv. 16:15:49 - RANGE NOT FOUND 14186059..14186249
30 janv. 16:15:49 - RANGE NOT FOUND 14186059..14186249
30 janv. 16:15:49 - RANGE NOT FOUND 14186059..14186249
30 janv. 16:15:49 - RANGE NOT FOUND 14183614..14183935
30 janv. 16:15:49 - RANGE NOT FOUND 38432069..38432092
30 janv. 16:15:49 - RANGE NOT FOUND 38421982..38422069
30 janv. 16:15:49 - RANGE NOT FOUND 38416927..38416953
30 janv. 16:15:49 - RANGE NOT FOUND 38407519..38407527
30 janv. 16:15:49 - RANGE NOT FOUND 38403192..38403197


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##gff-version 3
REF_EUCGR_scaffold0001  NCBI100 gene    11980   17630   .       +       .       
ID=GENE0;Dbxref=GeneID:104414021;Name=LOC104414021;gbkey=Gene;gene=LOC104414021;locus_tag=REF_EGR0001_GF00010_EUCGR
REF_EUCGR_scaffold0001  NCBI100 mRNA    11980   17630   .       +       .       
ID=RNA0;Parent=GENE0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Name=XM_010046065.1;Note=The
 sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;locus_tag=REF_EGR0001_TF00010.1_EUCGR;product=dnaJ
 protein ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 exon    11980   12154   .       +       .       
ID=ID1;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 exon    12668   12896   .       +       .       
ID=ID2;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 CDS     12711   12896   .       +       0       
ID=CDS0;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XP_010044367.1;Name=XP_010044367.1;Note=The
 sequence of the model RefSeq protein was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified translation 
discrepancy;gbkey=CDS;gene=LOC104414021;product=LOW QUALITY PROTEIN: dnaJ 
protein ERDJ2A-like;protein_id=XP_010044367.1
REF_EUCGR_scaffold0001  NCBI100 exon    12991   13086   .       +       .       
ID=ID3;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 CDS     12991   13086   .       +       0       
ID=CDS0;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XP_010044367.1;Name=XP_010044367.1;Note=The
 sequence of the model RefSeq protein was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified translation 
discrepancy;gbkey=CDS;gene=LOC104414021;product=LOW QUALITY PROTEIN: dnaJ 
protein ERDJ2A-like;protein_id=XP_010044367.1
REF_EUCGR_scaffold0001  NCBI100 exon    13275   13395   .       +       .       
ID=ID4;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 CDS     13275   13395   .       +       0       
ID=CDS0;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XP_010044367.1;Name=XP_010044367.1;Note=The
 sequence of the model RefSeq protein was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified translation 
discrepancy;gbkey=CDS;gene=LOC104414021;product=LOW QUALITY PROTEIN: dnaJ 
protein ERDJ2A-like;protein_id=XP_010044367.1
REF_EUCGR_scaffold0001  NCBI100 exon    13484   13590   .       +       .       
ID=ID5;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 CDS     13484   13590   .       +       2       
ID=CDS0;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XP_010044367.1;Name=XP_010044367.1;Note=The
 sequence of the model RefSeq protein was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified translation 
discrepancy;gbkey=CDS;gene=LOC104414021;product=LOW QUALITY PROTEIN: dnaJ 
protein ERDJ2A-like;protein_id=XP_010044367.1
REF_EUCGR_scaffold0001  NCBI100 exon    13670   13887   .       +       .       
ID=ID6;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 CDS     13670   13887   .       +       0       
ID=CDS0;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XP_010044367.1;Name=XP_010044367.1;Note=The
 sequence of the model RefSeq protein was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified translation 
discrepancy;gbkey=CDS;gene=LOC104414021;product=LOW QUALITY PROTEIN: dnaJ 
protein ERDJ2A-like;protein_id=XP_010044367.1
REF_EUCGR_scaffold0001  NCBI100 exon    14202   14379   .       +       .       
ID=ID7;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 CDS     14202   14379   .       +       1       
ID=CDS0;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XP_010044367.1;Name=XP_010044367.1;Note=The
 sequence of the model RefSeq protein was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified translation 
discrepancy;gbkey=CDS;gene=LOC104414021;product=LOW QUALITY PROTEIN: dnaJ 
protein ERDJ2A-like;protein_id=XP_010044367.1
REF_EUCGR_scaffold0001  NCBI100 exon    14480   14599   .       +       .       
ID=ID8;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 CDS     14480   14599   .       +       0       
ID=CDS0;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XP_010044367.1;Name=XP_010044367.1;Note=The
 sequence of the model RefSeq protein was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified translation 
discrepancy;gbkey=CDS;gene=LOC104414021;product=LOW QUALITY PROTEIN: dnaJ 
protein ERDJ2A-like;protein_id=XP_010044367.1
REF_EUCGR_scaffold0001  NCBI100 exon    14965   15051   .       +       .       
ID=ID9;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 CDS     14965   15051   .       +       0       
ID=CDS0;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XP_010044367.1;Name=XP_010044367.1;Note=The
 sequence of the model RefSeq protein was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified translation 
discrepancy;gbkey=CDS;gene=LOC104414021;product=LOW QUALITY PROTEIN: dnaJ 
protein ERDJ2A-like;protein_id=XP_010044367.1
REF_EUCGR_scaffold0001  NCBI100 exon    16064   16174   .       +       .       
ID=ID10;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 CDS     16064   16174   .       +       0       
ID=CDS0;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XP_010044367.1;Name=XP_010044367.1;Note=The
 sequence of the model RefSeq protein was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified translation 
discrepancy;gbkey=CDS;gene=LOC104414021;product=LOW QUALITY PROTEIN: dnaJ 
protein ERDJ2A-like;protein_id=XP_010044367.1
REF_EUCGR_scaffold0001  NCBI100 exon    16530   17630   .       +       .       
ID=ID11;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XM_010046065.1;Note=The 
sequence of the model RefSeq transcript was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified transcription 
discrepancy;gbkey=mRNA;gene=LOC104414021;product=dnaJ protein 
ERDJ2A-like;transcript_id=XM_010046065.1
REF_EUCGR_scaffold0001  NCBI100 CDS     16530   17350   .       +       0       
ID=CDS0;Parent=RNA0;Dbxref=GeneID:104414021,Genbank:XP_010044367.1;Name=XP_010044367.1;Note=The
 sequence of the model RefSeq protein was modified relative to this genomic 
sequence to represent the inferred CDS: inserted 1 base in 1 
codon;exception=unclassified translation 
discrepancy;gbkey=CDS;gene=LOC104414021;product=LOW QUALITY PROTEIN: dnaJ 
protein ERDJ2A-like;protein_id=XP_010044367.1

<<attachment: stephanie_sidibe-bocs.vcf>>

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