[ensembl-dev] ensembl-compara pipeline problems
江文恺
jiangwenkai at mail.kib.ac.cn
Mon Oct 25 10:20:06 BST 2010
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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