Hi,<div>The problem is solved by change codes in C<span class="Apple-style-span" style="font-family: monospace; white-space: pre-wrap; ">reateAlignmentChainsJobs.pm</span></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="white-space: pre-wrap;">By using <span class="Apple-style-span" style="font-family: sans-serif; white-space: normal; font-size: 13px; ">fetch_by_logic_name('AlignmentChains'), the pipeline continues, </span></span></font></div><div><font class="Apple-style-span" face="monospace"><span class="Apple-style-span" style="white-space: pre-wrap;"><span class="Apple-style-span" style="font-family: sans-serif; white-space: normal; font-size: 13px; ">possibly this feature is unique to 2x alignments?</span></span></font><span class="Apple-style-span" style="font-family: sans-serif; font-size: 13px; "> </span></div><div><br><table cellspacing="0" cellpadding="0" style="width: 1624px; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; border-top-style: none; border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; font-family: 'Times New Roman'; font-size: medium; "><tbody><tr style="vertical-align: top; "><td id="l202" style="vertical-align: top; "><a href="/cgi-bin/viewvc.cgi/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentChainsJobs.pm?annotate=1.9.26.1&root=ensembl#l202" style="color: rgb(0, 0, 255); ">202</a></td><td class="vc_diff_nochange" style="vertical-align: top; font-family: sans-serif; font-size: smaller; "> sub createAlignmentChainsJobs</td><td class="vc_diff_nochange" style="vertical-align: top; font-family: sans-serif; font-size: smaller; "> sub createAlignmentChainsJobs</td></tr><tr style="vertical-align: top; "><td id="l203" style="vertical-align: top; "><a href="/cgi-bin/viewvc.cgi/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentChainsJobs.pm?annotate=1.9.26.1&root=ensembl#l203" style="color: rgb(0, 0, 255); ">203</a></td><td class="vc_diff_nochange" style="vertical-align: top; font-family: sans-serif; font-size: smaller; "> {</td><td class="vc_diff_nochange" style="vertical-align: top; font-family: sans-serif; font-size: smaller; "> {</td></tr><tr style="vertical-align: top; "><td id="l204" style="vertical-align: top; "><a href="/cgi-bin/viewvc.cgi/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentChainsJobs.pm?annotate=1.9.26.1&root=ensembl#l204" style="color: rgb(0, 0, 255); ">204</a></td><td class="vc_diff_nochange" style="vertical-align: top; font-family: sans-serif; font-size: smaller; ">   my $self = shift;</td><td class="vc_diff_nochange" style="vertical-align: top; font-family: sans-serif; font-size: smaller; ">   my $self = shift;</td></tr><tr style="vertical-align: top; "><td id="l205" style="vertical-align: top; "><a href="/cgi-bin/viewvc.cgi/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentChainsJobs.pm?annotate=1.9.26.1&root=ensembl#l205" style="color: rgb(0, 0, 255); ">205</a></td><td class="vc_diff_change" style="vertical-align: top; background-color: rgb(255, 255, 119); font-family: sans-serif; font-size: smaller; "> </td><td class="vc_diff_change" style="vertical-align: top; background-color: rgb(255, 255, 119); font-family: sans-serif; font-size: smaller; ">   #print "CREATING ALIGNMENT CHAIN JOBS \n" ;</td></tr><tr style="vertical-align: top; "><td id="l206" style="vertical-align: top; "><a href="/cgi-bin/viewvc.cgi/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentChainsJobs.pm?annotate=1.9.26.1&root=ensembl#l206" style="color: rgb(0, 0, 255); ">206</a></td><td class="vc_diff_change" style="vertical-align: top; background-color: rgb(255, 255, 119); font-family: sans-serif; font-size: smaller; ">   #my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name('AlignmentChains');</td><td class="vc_diff_change" style="vertical-align: top; background-color: rgb(255, 255, 119); font-family: sans-serif; font-size: smaller; ">   my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name('AlignmentChains');</td></tr><tr style="vertical-align: top; "><td id="l207" style="vertical-align: top; "><a href="/cgi-bin/viewvc.cgi/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentChainsJobs.pm?annotate=1.9.26.1&root=ensembl#l207" style="color: rgb(0, 0, 255); ">207</a></td><td class="vc_diff_change" style="vertical-align: top; background-color: rgb(255, 255, 119); font-family: sans-serif; font-size: smaller; ">   my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($self->{'logic_name'});</td><td class="vc_diff_change" style="vertical-align: top; background-color: rgb(255, 255, 119); font-family: sans-serif; font-size: smaller; ">   # SMJS Reverted recent change for 2x my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($self->{'logic_name'});</td></tr><tr style="vertical-align: top; "><td id="l208" style="vertical-align: top; "><a href="/cgi-bin/viewvc.cgi/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentChainsJobs.pm?annotate=1.9.26.1&root=ensembl#l208" style="color: rgb(0, 0, 255); ">208</a></td><td class="vc_diff_nochange" style="vertical-align: top; font-family: sans-serif; font-size: smaller; "> </td><td class="vc_diff_nochange" style="vertical-align: top; font-family: sans-serif; font-size: smaller; "> </td></tr><tr style="vertical-align: top; "><td id="l209" style="vertical-align: top; "><a href="/cgi-bin/viewvc.cgi/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentChainsJobs.pm?annotate=1.9.26.1&root=ensembl#l209" style="color: rgb(0, 0, 255); ">209</a></td><td class="vc_diff_nochange" style="vertical-align: top; font-family: sans-serif; font-size: smaller; ">   my (%qy_dna_hash, %tg_dna_hash);</td><td class="vc_diff_nochange" style="vertical-align: top; font-family: sans-serif; font-size: smaller; ">   my (%qy_dna_hash, %tg_dna_hash);</td></tr></tbody></table><blockquote style="padding-left:5px;margin-left:5px;border-left:#a0c6e5 2px solid;margin-right:0">-----原始邮件-----<br>
<b>发件人:</b> "江文恺" <jiangwenkai@mail.kib.ac.cn><br>
<b>发送时间:</b> 2010年10月25日 星期一<br>
<b>收件人:</b> dev@ensembl.org<br>
<b>抄送:</b> <br>
<b>主题:</b> Re: [ensembl-dev] ensembl-compara pipeline problems<br><br>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, 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
> <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
> <a target="_blank" href="http://lists.ensembl.org/mailman/listinfo/dev" style="text-decoration: none; color: rgb(56, 148, 193); ">http://lists.ensembl.org/mailman/listinfo/dev</a>
</pre><div><br></div></div><br></div></div><br><br>

</blockquote><br><span></span></div><br><br>