[Bioperl-l] [Gmod-gbrowse] Landmark not recognized SeqFeature::Store database problem
Scott Cain
scott at scottcain.net
Tue Jan 25 22:36:07 UTC 2011
Hi Darwin,
In column 9, case matters. That is, "name" != "Name". Try changing
that for the scaffold.
Scott
On Tue, Jan 25, 2011 at 4:59 PM, Darwin Sorento Dichmann
<dichmann at berkeley.edu> wrote:
> 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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--
------------------------------------------------------------------------
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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