[ensembl-dev] ensembl-compara pipeline problems
Jan-hinnerk Vogel
jhv at sanger.ac.uk
Mon Oct 25 17:28:53 BST 2010
Hi Wenkai,
well spotted - let us know if you run into further problems .
Regards,
Jan
On 25 Oct 2010, at 16:32, 江文恺 wrote:
> Hi,
> The problem is solved by change codes in CreateAlignmentChainsJobs.pm
> By using fetch_by_logic_name('AlignmentChains'), the pipeline
> continues,
> possibly this feature is unique to 2x alignments?
>
> 202
> sub createAlignmentChainsJobs
> sub createAlignmentChainsJobs
> 203
> {
> {
> 204
> my $self = shift;
> my $self = shift;
> 205
>
> #print "CREATING ALIGNMENT CHAIN JOBS \n" ;
> 206
> #my $analysis = $self->db->get_AnalysisAdaptor-
> >fetch_by_logic_name('AlignmentChains');
> my $analysis = $self->db->get_AnalysisAdaptor-
> >fetch_by_logic_name('AlignmentChains');
> 207
> my $analysis = $self->db->get_AnalysisAdaptor-
> >fetch_by_logic_name($self->{'logic_name'});
> # SMJS Reverted recent change for 2x my $analysis = $self->db-
> >get_AnalysisAdaptor->fetch_by_logic_name($self->{'logic_name'});
> 208
>
>
> 209
> my (%qy_dna_hash, %tg_dna_hash);
> my (%qy_dna_hash, %tg_dna_hash);
> -----原始邮件-----
> 发件人: "江文恺" <jiangwenkai at mail.kib.ac.cn>
> 发送时间: 2010年10月25日 星期一
> 收件人: dev at ensembl.org
> 抄送:
> 主题: Re: [ensembl-dev] ensembl-compara pipeline problems
>
> Hi,
>
> The code is check out as follows:
> ensembl-compara HEAD
> ensembl-hive HEAD
> ensembl-pipeline HEAD
> ensembl-analysis HEAD
> ensembl branch59
>
>
> -----------------------------------------------
> 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, 江文恺 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
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Dev mailing list
> > Dev at ensembl.org
> > http://lists.ensembl.org/mailman/listinfo/dev
>
>
>
>
>
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
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