Hi,<div><br></div><div>The code is check out as follows:</div><div>ensembl-compara HEAD</div><div>ensembl-hive HEAD</div><div>ensembl-pipeline HEAD</div><div>ensembl-analysis HEAD</div><div>ensembl branch59</div><div><br></div><div><div><br></div><div>-----------------------------------------------<br><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 12px; font-family: tahoma, verdana, arial, helvetica, sans-serif; "><pre wrap="soft" style="word-wrap: break-word; ">Hi Wenkai,
which checkout of the ensembl-compara code are you using ? Are you
running on the head code or
did you specify a specific branch to be checked out ?
Regards,
Jan
On 25 Oct 2010, at 10:20, ½ÎÄâý wrote:
> Hi, all,
>
> I have try to align 2 genomes under ensembl-compara pipeline, which
> use the guide of 2x genome alignment,
>
> I successfully run several alignments, but the step
> CreateAlignmentChainsJobs (16) Fails,
>
>
>
> The output for this is:
>
> SubmitGenome ( 1) DONE 0:cpum job(0/2 run:0
> fail:0 23ms) worker[0/-1] (sync'd 1 sec ago)
>
> ChunkAndGroupDna ( 2) DONE 0:cpum job(0/2 run:0
> fail:0 9922ms) worker[0/-1] (sync'd 1 sec ago)
>
> StoreSequence ( 3) DONE 0:cpum job(0/127 run:0
> fail:0 98747ms) worker[0/100] (sync'd 1 sec ago)
>
> CreatePairAlignerJobs ( 4) DONE 0:cpum job(0/2 run:0
> fail:0 3954ms) worker[0/1] (sync'd 1 sec ago)
>
> BlastZ-29e37998 ( 5) DONE 0:cpum job(0/3432 run:0
> fail:0 438961ms) worker[0/600] (sync'd 1 sec ago)
>
> DumpDnaForBlastZ-29e37998 ( 6) DONE 0:cpum job(0/1 run:0
> fail:0 30734ms) worker[0/1] (sync'd 1 sec ago)
>
> UpdateMaxAlignmentLengthBeforeFD( 7) DONE 0:cpum job(0/1 run:
> 0 fail:0 865113ms) worker[0/1] (sync'd 1 sec ago)
>
> QueryFilterDuplicates-29e37998( 8) DONE 0:cpum job(0/15858
> run:0 fail:0 94187ms) worker[0/50] (sync'd 1 sec ago)
>
> UpdateMaxAlignmentLengthAfterFD( 9) DONE 0:cpum job(0/1 run:0
> fail:0 339076ms) worker[0/1] (sync'd 1 sec ago)
>
> CreateFilterDuplicatesJobs (10) DONE 0:cpum job(0/4 run:0
> fail:0 7680ms) worker[0/600] (sync'd 1 sec ago)
>
> TargetFilterDuplicates-29e37998(11) DONE 0:cpum job(0/16 run:
> 0 fail:0 572916ms) worker[0/200] (sync'd 1 sec ago)
>
> BlastZ-2782424c (12) DONE 0:cpum job(0/3432 run:0
> fail:0 629626ms) worker[0/600] (sync'd 1 sec ago)
>
> DumpDnaForBlastZ-2782424c (13) DONE 0:cpum job(0/1 run:0
> fail:0 32078ms) worker[0/1] (sync'd 1 sec ago)
>
> QueryFilterDuplicates-2782424c(14) DONE 0:cpum job(0/15858
> run:0 fail:0 1014ms) worker[0/50] (sync'd 1 sec ago)
>
> TargetFilterDuplicates-2782424c(15) DONE 0:cpum job(0/16 run:
> 0 fail:0 679609ms) worker[0/200] (sync'd 1 sec ago)
>
> CreateAlignmentChainsJobs (16) FAILED 0:cpum job(0/1 run:0
> fail:1 0ms) worker[0/1] (sync'd 1 sec ago)
>
> AlignmentChains (17) BLOCKED 0:cpum job(0/0 run:0
> fail:0 0ms) worker[0/600] (sync'd 1 sec ago)
>
> UpdateMaxAlignmentLengthAfterChain(18) BLOCKED 0:cpum job(0/0
> run:0 fail:0 0ms) worker[0/1] (sync'd 1 sec ago)
>
> Net-ContigAwareNet (19) BLOCKED 0:cpum job(0/0 run:0
> fail:0 0ms) worker[0/600] (sync'd 1 sec ago)
>
> CreateAlignmentNetsJobs (20) BLOCKED 0:cpum job(1/1 run:0
> fail:0 0ms) worker[1/1] (sync'd 1 sec ago)
>
> UpdateMaxAlignmentLengthAfterNet(21) BLOCKED 0:cpum job(0/0 run:
> 0 fail:0 0ms) worker[0/1] (sync'd 1 sec ago)
>
>
>
>
>
> Then i check the error output for the this job, which show me that:
>
>
>
> Job with id=38754 died in status 'RUN' for the following reason:
> -------------------- EXCEPTION --------------------
> MSG: must define analysis
> STACK Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::CreateNewJob /
> home/SCE/jiangwenkai/ensembl/ensembl-hive/modules/Bio/EnsEMBL/Hive/DB
> SQL/AnalysisJobAdaptor.pm:90
> STACK
> Bio
> ::EnsEMBL
> ::Compara
> ::Production
> ::GenomicAlignBlock
> ::CreateAlignmentChainsJobs::createAlignmentChainsJobs /home/SCE/
> jiangwenkai/e
> nsembl/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/
> GenomicAlignBlock/CreateAlignmentChainsJobs.pm:281
> STACK
> Bio
> ::EnsEMBL
> ::Compara
> ::Production::GenomicAlignBlock::CreateAlignmentChainsJobs::run /
> home/SCE/jiangwenkai/ensembl/ensembl-compara
> /modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/
> CreateAlignmentChainsJobs.pm:132
> STACK Bio::EnsEMBL::Hive::Worker::run_module_with_job /home/SCE/
> jiangwenkai/ensembl/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:
> 698
> STACK (eval) /home/SCE/jiangwenkai/ensembl/ensembl-hive/modules/Bio/
> EnsEMBL/Hive/Worker.pm:607
> STACK Bio::EnsEMBL::Hive::Worker::run_one_batch /home/SCE/
> jiangwenkai/ensembl/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:
> 606
> STACK Bio::EnsEMBL::Hive::Worker::run /home/SCE/jiangwenkai/ensembl/
> ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:518
> STACK toplevel /home/SCE/jiangwenkai/ensembl/ensembl-hive/scripts/
> runWorker.pl:140
> ---------------------------------------------------
>
> All the code is similar to the examples 2x-alignment configuration
> files, so how could this error occurs?
>
> The different might be that my query genomes dose not have
> chromosomes, just lots of contigs range from 1kb ~ 300kb.
>
>
>
> the setting for my configuration is like:
>
>
>
> { TYPE => PAIR_ALIGNER,
>
>
>
> logic_name_prefix => 'BlastZ',
>
> method_link => [10, 'BLASTZ_RAW'],
>
> analysis_template => {
>
> -program => 'blastz',
>
> -parameters => "{method_link=>'BLASTZ_RAW',options=>'T=1
> L=3000 H=2200 M=40000000 O=400 E=30'}",
>
> -module =>
> 'Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::BlastZ',
>
> },
>
>
>
> query_collection_name => 'oga genome',
>
> target_collection_name => 'rice genome',
>
> filter_duplicates_options => 'all',
>
> # set the following to about 50 to be kind to the mysql instances
>
>
>
> # optional; default batch-size = 1, 3 is optimal for blastz
>
> batch_size => 1,
>
> max_parallel_workers => 600,
>
>
>
> },
>
>
>
> { TYPE => CHAIN_CONFIG,
>
> method_link => [2001, 'HIVE_CHAIN'],
>
> input_method_link_type => 'BLASTZ_RAW',
>
>
>
> query_collection_name => 'oga genome',
>
> target_collection_name => 'rice genome',
>
>
>
> max_gap => 50,
>
>
>
> max_parallel_workers => 600,
>
> },
>
>
>
> #
>
> # set-up for alignment nets
>
> #
>
> {
>
> TYPE => NET_CONFIG,
>
>
>
> method_link => [3001, 'CONTIG_AWARE_NET'],
>
> input_method_link_type => 'HIVE_CHAIN',
>
>
>
> net_method => 'ContigAwareNet',
>
>
>
> query_collection_name => 'oga genome',
>
> target_collection_name => 'rice genome',
>
>
>
> max_gap => 50,
>
>
>
> max_parallel_workers => 600,
>
> },
>
>
>
> Possbily i must add " analysis_template " to the CHAIN_CONFIG and
> NET_CONFIG? but if so, are there some templates.
>
>
>
> Thanks for all!
>
>
>
> Wenkai
>
>
>
>
>
>
>
>
>
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</pre><div><br></div></div><br></div></div><br><br>