Hi<br> I'm trying to use the lowcoverage annotation pipeline. At first,
after reading docs in ensembl-doc/pipeline-docs, I found that I have to
construct a compara database containing the whole-genome-alignment
results. Then I checkouted ensembl-compara and ensembl-hive, tried to
run the wga pipeline according to the following steps:<br>
1. downloaded the reference genome mysql files from ensembl, which works fine.<br> 2. prepared my interested genome according the guide in ensembl-doc/loading_sequence_<div>into_ensembl.txt. still seems fine.<br clear="all">
3. prepared conf file and run comparaLoadGenomes.pl and loadPairAlignerSystem.pl. the tables in compara database seems fine.<br> 4. run <a href="http://beekeeper.pl/" target="_blank">beekeeper.pl</a>.
problem ocurs for the second analysis ChunkAndGroupDNA, there are two
jobs to run, one for the reference genome and the other for my
interested genome. The ref genome loaded correctly while no data refer
to my intersted genome loade in dnafrag, dnafrag_chunk and
dna_collection tables. One line in the job_id_3.out (the job id for
ChunkAndGroupDNA for my interested genome) file is: number of
seq_regions 0<br>
<br> The problem seemed that the pipeline failed to see my genome
data. Should I add some special info to the meta table for my interest
genome database? <br><br> Thank you.</div><br clear="all"><br>-- <br>Zhang Di<br>