[Bioperl-l] Landmark not recognized SeqFeature::Store database problem

[Darwin Sorento Dichmann]

Hello,

I am trying to set up a SeqFeature::Store database. However, I consistently get "Landmark named scaffold_something is not recognized. See the help pages for suggestions." Apache errorlog shows nothing. I am currently troubleshooting on a single scaffold and get same error.

I've been banging my head against this for weeks and can't figure out what the problem is. Any help or pointers are greatly appreciated. Cc'ed to the bioperl list.

Best wishes,
Darwin 

The database seem to load properly and I can find the scaffold name:
---
mysql> select seqname from locationlist;
+--------------+
| seqname      |
+--------------+
| scaffold_498 |
+--------------+
---
Command for loading the database and head of files: 
-----
bp_seqfeature_load.pl -dsn frog3 -u darwin -p xxxxxxx -c -v fixed_scaffold_498.gff3 scaffold_498.fasta
loading scaffold_498.gff3...
Building object tree... 0.00s                                                                              
load time:  0.02s
loading scaffold_498.fasta...
Building object tree... 0.00s                                                                              
load time:  0.28s


Macintosh:scaffold_498 darwin$ head -25 fixed_scaffold_498.gff3 
scaffold_498	pick	scaffold	1	875342	.	.	.	name=scaffold_498
scaffold_498	pick	gene	5249	38060	1000	+	.	ID=CUFF.398955;Name=
scaffold_498	pick	transcript	5249	38060	1000	+	.	ID=CUFF.398955.1;Name=;Parent=CUFF.398955
scaffold_498	pick	exon	5249	5359	1000	+	.	ID=CUFF.398955.1.1;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	5508	5661	1000	+	.	ID=CUFF.398955.1.2;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	7474	7647	1000	+	.	ID=CUFF.398955.1.3;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	7819	8005	1000	+	.	ID=CUFF.398955.1.4;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	8254	8419	1000	+	.	ID=CUFF.398955.1.5;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	9997	10111	1000	+	.	ID=CUFF.398955.1.6;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	12104	12302	1000	+	.	ID=CUFF.398955.1.7;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	13854	13954	1000	+	.	ID=CUFF.398955.1.8;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	14810	14989	1000	+	.	ID=CUFF.398955.1.9;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	15310	15394	1000	+	.	ID=CUFF.398955.1.10;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	15938	16044	1000	+	.	ID=CUFF.398955.1.11;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	17997	18072	1000	+	.	ID=CUFF.398955.1.12;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	18364	18472	1000	+	.	ID=CUFF.398955.1.13;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	19364	19488	1000	+	.	ID=CUFF.398955.1.14;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	21402	21549	1000	+	.	ID=CUFF.398955.1.15;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	27620	27726	1000	+	.	ID=CUFF.398955.1.16;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	29322	29436	1000	+	.	ID=CUFF.398955.1.17;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	29958	30129	1000	+	.	ID=CUFF.398955.1.18;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	30947	31055	1000	+	.	ID=CUFF.398955.1.19;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	31247	31309	1000	+	.	ID=CUFF.398955.1.20;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	31461	31526	1000	+	.	ID=CUFF.398955.1.21;Name=;Parent=CUFF.398955.1
scaffold_498	pick	exon	32478	32625	1000	+	.	ID=CUFF.398955.1.22;Name=;Parent=CUFF.398955.1

Macintosh:scaffold_498 darwin$ head -25 scaffold_498.fasta 
>scaffold_498
TAATATTGTGATGGTCGGCCCTGTAGCTCCTGCTCTAATACAGAACCATTTTCCATTGTG
GTTTTCCAGTGAGATAAACCCTTAATCAAACTGCATAATAAACTGACGGTAGCACACTAG
CACTGGCTGTATCCCTTCTTGAGTAAAAAAAATAAATGGATCTGCCCTTGCTCTTTACCT
CATTAGGCCAGTGGAGTAGATTTGGCATTGGATCATAGCAACGTATGTTTCCAACACAAG
TGACACATTGCTGATTCAGTCCATCTTGACCAGGGCAAAGTTATTAGGTCATATATGGAG
TGAAAACAATGGATTTCCCTACTATTATCTAATCTGGGCTTGTTTGGATATGGATTGGGC
AAGCTGGAAATTGCCATTGGCTGAGGATCATATCAGGCTGTGGAGGCAGCCCATGAACAA
AAGGTCTTCATGAGCTTTTTAAATGATCATATTATTTCAGCCAAGCTTGACCCAACACTA
AGGTGGCTAAATGGGACGGAAGAGTTCTTGCGTGGCAGCAAAAATGAGACGGATCTTCTC
AAACTGCACAGCTTTAATTCTTAGAACATGTTTTCCTAGAGGTCAATACTTTGCATGTCT
GAGTTACCACATGATCGACTCAATCCCATGCTGTAGCCCTCAAGCTCACTGAGCCTTATT
ATCTTATTATTTATACTCTGTAGCCTCTTTGGTGCCAAATGTTCTATTGCATAGATGGCA
CAGGGTAACTTTCTGAGTGAGGTTCCTCAGAAATAAATTGAATATATGTCTGCGCTGCTG
ATGCTTAAAGTTTGGCTTGGGAACCCCACATTGGCACACTATTTATAGCCAGTGAGAGGT
AATTGCTAATATGAAGTGGATTGCCAAACTCATTCTATTTTGGATCACAGAGTGGTACat
acaggtatgggacccgttattcagaatgctcgggaccaagggtattctggataaggggtc
tttccgtaatttggatctccatacattaagtccactaaaaaatcaataaaacgttaataa
aacccagtaggactgttctgccccaataaagattaattatattttagttgggatcaagta
caggtactgttttattattacagagaaaagggaatcatttaaccattaaataaacccaat
aggactgttctgcccccaataaggggtaattatatcttagttgggatcaagtacaggtac
tgttttattattacagagaaaagggaatcatttaaccattaaataaacccaataggactg
ttctgcccccaataaggggtaattatatcttagttgggatcaagtacaggtactgtttta
ttattacAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCA


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