<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 12px; font-family: tahoma, verdana, arial, helvetica, sans-serif; ">
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">Hi,
all,</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">I
have try to align 2 genomes under ensembl-compara pipeline, which use
the guide of 2x genome alignment,</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">I
successfully run several alignments, but the
step CreateAlignmentChainsJobs (16) Fails,</span></font></font></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">The
output for this is:</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">SubmitGenome
( 1)
DONE 0:cpum job(0/2 run:0 fail:0 23ms) worker[0/-1] (sync'd 1
sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">ChunkAndGroupDna
( 2) DONE
0:cpum job(0/2 run:0 fail:0 9922ms) worker[0/-1] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">StoreSequence
( 3)
DONE 0:cpum job(0/127 run:0 fail:0 98747ms) worker[0/100]
(sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">CreatePairAlignerJobs
( 4) DONE 0:cpum
job(0/2 run:0 fail:0 3954ms) worker[0/1] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">BlastZ-29e37998
( 5)
DONE 0:cpum job(0/3432 run:0 fail:0 438961ms) worker[0/600]
(sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">DumpDnaForBlastZ-29e37998
( 6) DONE 0:cpum job(0/1 run:0
fail:0 30734ms) worker[0/1] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">UpdateMaxAlignmentLengthBeforeFD(
7) DONE 0:cpum job(0/1 run:0 fail:0
865113ms) worker[0/1] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">QueryFilterDuplicates-29e37998(
8) DONE 0:cpum job(0/15858 run:0 fail:0
94187ms) worker[0/50] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">UpdateMaxAlignmentLengthAfterFD(
9) DONE 0:cpum job(0/1 run:0 fail:0
339076ms) worker[0/1] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">CreateFilterDuplicatesJobs
(10) DONE 0:cpum job(0/4 run:0 fail:0
7680ms) worker[0/600] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">TargetFilterDuplicates-29e37998(11)
DONE 0:cpum job(0/16 run:0 fail:0
572916ms) worker[0/200] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">BlastZ-2782424c
(12)
DONE 0:cpum job(0/3432 run:0 fail:0 629626ms) worker[0/600]
(sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">DumpDnaForBlastZ-2782424c
(13) DONE 0:cpum job(0/1 run:0
fail:0 32078ms) worker[0/1] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">QueryFilterDuplicates-2782424c(14)
DONE 0:cpum job(0/15858 run:0 fail:0
1014ms) worker[0/50] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">TargetFilterDuplicates-2782424c(15)
DONE 0:cpum job(0/16 run:0 fail:0
679609ms) worker[0/200] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">CreateAlignmentChainsJobs
(16) FAILED 0:cpum job(0/1 run:0 fail:1
0ms) worker[0/1] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">AlignmentChains
(17) BLOCKED
0:cpum job(0/0 run:0 fail:0 0ms) worker[0/600] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">UpdateMaxAlignmentLengthAfterChain(18)
BLOCKED 0:cpum job(0/0 run:0 fail:0 0ms) worker[0/1]
(sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">Net-ContigAwareNet
(19) BLOCKED 0:cpum job(0/0
run:0 fail:0 0ms) worker[0/600] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">CreateAlignmentNetsJobs
(20) BLOCKED 0:cpum job(1/1 run:0 fail:0
0ms) worker[1/1] (sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">UpdateMaxAlignmentLengthAfterNet(21)
BLOCKED 0:cpum job(0/0 run:0 fail:0 0ms) worker[0/1]
(sync'd 1 sec ago)</span></font></font></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">Then
i check the error output for the this job, which show me that:</span></font></font></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">Job with id=38754 died in status 'RUN' for the following reason: <br>-------------------- EXCEPTION --------------------<br>MSG: must define analysis<br>STACK Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::CreateNewJob /home/SCE/jiangwenkai/ensembl/ensembl-hive/modules/Bio/EnsEMBL/Hive/DB<br>SQL/AnalysisJobAdaptor.pm:90<br>STACK Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateAlignmentChainsJobs::createAlignmentChainsJobs /home/SCE/jiangwenkai/e<br>nsembl/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentChainsJobs.pm:281<br>STACK Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateAlignmentChainsJobs::run /home/SCE/jiangwenkai/ensembl/ensembl-compara<br>/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentChainsJobs.pm:132<br>STACK Bio::EnsEMBL::Hive::Worker::run_module_with_job /home/SCE/jiangwenkai/ensembl/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:698<br>STACK (eval) /home/SCE/jiangwenkai/ensembl/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:607<br>STACK Bio::EnsEMBL::Hive::Worker::run_one_batch /home/SCE/jiangwenkai/ensembl/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:606<br>STACK Bio::EnsEMBL::Hive::Worker::run /home/SCE/jiangwenkai/ensembl/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:518<br>STACK toplevel /home/SCE/jiangwenkai/ensembl/ensembl-hive/scripts/runWorker.pl:140<br>---------------------------------------------------<br><br>All
the code is similar to the examples 2x-alignment configuration files,
so how could this error occurs?</span></font></font></font></p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">The
different might be that my query genomes dose not have chromosomes,
just lots of contigs range from 1kb ~ 300kb.</span></font></font></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">the
setting for my configuration is like:</span></font></font></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff"> <font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">{
TYPE => PAIR_ALIGNER,</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">logic_name_prefix
=> 'BlastZ',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">method_link
=> [10, 'BLASTZ_RAW'],</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">analysis_template
=> {</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">-program
=> 'blastz',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">-parameters
=> "{method_link=>'BLASTZ_RAW',options=>'T=1 L=3000
H=2200 M=40000000 O=400 E=30'}",</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">-module
=>
'Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::BlastZ',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">},</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">query_collection_name
=> 'oga genome',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">target_collection_name
=> 'rice genome',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">filter_duplicates_options
=> 'all',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">#
set the following to about 50 to be kind to the mysql instances</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">#
optional; default batch-size = 1, 3 is optimal for blastz</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">batch_size
=> 1,</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">max_parallel_workers
=> 600,</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff"> <font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">},</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff"> <font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">{
TYPE => CHAIN_CONFIG,</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">method_link
=> [2001, 'HIVE_CHAIN'],</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">input_method_link_type
=> 'BLASTZ_RAW',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">query_collection_name
=> 'oga genome',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">target_collection_name
=> 'rice genome',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">max_gap
=> 50,</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">max_parallel_workers
=> 600,</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff"> <font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">},</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff"> <font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">#</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff"> <font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">#
set-up for alignment nets</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff"> <font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">#</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff"> <font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">{</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">TYPE
=> NET_CONFIG,</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">method_link
=> [3001, 'CONTIG_AWARE_NET'],</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">input_method_link_type
=> 'HIVE_CHAIN',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">net_method
=> 'ContigAwareNet',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">query_collection_name
=> 'oga genome',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">target_collection_name
=> 'rice genome',</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">max_gap
=> 50,</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff">
<font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">max_parallel_workers
=> 600,</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><font color="#000000"><span style="background: #ffffff"> <font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: medium">},</span></span></font></font></span></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">Possbily
i must add " analysis_template " to the CHAIN_CONFIG
and NET_CONFIG? but if so, are there some templates.</span></font></font></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">Thanks
for all!</span></font></font></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; font-style: normal; font-weight: medium; widows: 2; orphans: 2">
<font color="#000000"><font face="tahoma, verdana, arial, helvetica, sans-serif"><font size="2" style="font-size: 9pt"><span style="background: #ffffff">Wenkai</span></font></font></font></p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in; widows: 2; orphans: 2"><br>
</p>
<p style="margin-bottom: 0in"><br>
</p>
</div><br><br>