[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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