<div><font face="arial,helvetica,sans-serif">Hi, </font></div>
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<div>I'm having trouble running an analysis. Whatever pipeline step is running, I'm getting "Null submission ID.." errors, such as:</div>
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<div><font face="courier new,monospace">FILE: EnsEMBL/Pipeline/Job.pm LINE: 396<br>CALLED BY: EnsEMBL/Pipeline/Job.pm LINE: 492<br>Ensembl API version = 64<br>---------------------------------------------------<br>Job: Null submission ID for the following, but continuing: 91 92 94 95 97 98 100 101 103 104<br>
Job: Null submission ID for the following, but continuing: 91 92 94 95 97 98 100 101 103 104<br>Job: Null submission ID for the following, but continuing: 91 92 94 95 97 98 100 101 103 104<br>Job: Null submission ID for the following, but continuing: 91 92 94 95 97 98 100 101 103 104<br>
Job: Null submission ID for the following, but continuing: 91 92 94 95 97 98 100 101 103 104<br>Job: Null submission ID for the following, but continuing: 91 92 94 95 97 98 100 101 103 104<br>Job: Null submission ID for the following, but continuing: 91 92 94 95 97 98 100 101 103 104<br>
Job: Null submission ID for the following, but continuing: 91 92 94 95 97 98 100 101 103 104<br>Job: Null submission ID for the following, but continuing: 91 92 94 95 97 98 100 101 103 104<br>Job: Null submission ID for the following, but continuing: 91 92 94 95 97 98 100 101 103 104</font><br>
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<div>I'm guessing there is something wrong with the way I create the input id's, so here are the commands I run: </div>
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<div><font face="courier new,monospace">./<a href="http://analysis_setup.pl/" target="_blank">analysis_setup.pl</a> -dbhost localhost -dbuser ensembl -dbpass ************** -dbname drosophila_americana_h5_core_64 -read -file /usr/local/ensembl/genebuild/configs/analysis.conf</font></div>
<div><font face="courier new,monospace"></font> </div>
<div><font face="courier new,monospace">./<a href="http://rule_setup.pl/" target="_blank">rule_setup.pl</a> -dbhost localhost -dbuser ensembl -dbpass ************ -dbname drosophila_americana_h5_core_64 -read -file /usr/local/ensembl/genebuild/configs/rules.conf</font></div>
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<div><font face="courier new,monospace">./make_input_ids -dbhost localhost -dbuser ensembl -dbpass ****** -dbname drosophila_americana_h5_core_64 -slice -seq_level -coord_system scaffold -logic_name SubmitScaffold</font></div>
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<div><font face="courier new,monospace">nohup ./<a href="http://rulemanager.pl/" target="_blank">rulemanager.pl</a> -dbhost localhost -dbuser ensembl -dbpass ********* -dbname drosophila_americana_h5_core_64 &</font></div>
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<div>The analysis and rules configurations are below.</div>
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<div>The database has two coordinate systems: scaffold and chunk.</div>
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<div>I've read and followed the "quick_start_pipeline_guide.txt" instructions and the other files on pipeline-docs, but didn't find an answer :\</div>
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<div>Could you please help me?</div>
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<div>Thank you,</div>
<div>Diogo Costa</div>
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<div><font face="courier new,monospace">Analysis.conf</font></div>
<div><font face="courier new,monospace"></font> </div>
<div><font face="courier new,monospace">[Eponine]<br>db=eponine<br>program=eponine-scan<br>program_file=/usr/bin/java<br>parameters=-epojar => /usr/local/ensembl/programs/eponine/eponine-scan.jar, -threshold => 0.999<br>
module=EponineTSS<br>input_id_type=SCAFFOLD</font></div>
<p><font face="courier new,monospace">[RepeatMask]<br>db=repbase<br>db_version=20090604<br>db_file=repbase<br>program=RepeatMasker<br>program_version=open-3.3.0<br>program_file=/usr/local/ensembl/programs/RepeatMasker/RepeatMasker<br>
parameters=-nolow -species "drosophila virilis" -s<br>module=RepeatMasker<br>gff_source=RepeatMask<br>gff_feature=repeat<br>input_id_type=SCAFFOLD</font></p>
<p><font face="courier new,monospace">[SubmitScaffold]<br>input_id_type=SCAFFOLD<br>module=Dummy</font></p>
<p><font face="courier new,monospace">[UniGene]<br>db=Dm_seq_all.fasta<br>db_file=/usr/local/ensembl/unigene/Dm_seq_all.fasta<br>program=tblastn<br>program_file=/usr/local/ensembl/programs/rmblast/bin/tblastn<br>parameters=-cpus => 1, -hitdist => 40<br>
module=BlastGenscanDNA<br>input_id_type=SCAFFOLD</font></p>
<p><br><font face="courier new,monospace">[Genscan]<br>db=/usr/local/ensembl/programs/genscan/HumanIso.smat<br>db_file=/usr/local/ensembl/programs/genscan/HumanIso.smat<br>program_file=genscan<br>module=Genscan<br>input_id_type=SCAFFOLD</font></p>
<p><br><font face="courier new,monospace">[TRF]<br>program_file=/usr/local/ensembl/programs/trf/trf<br>module=TRF<br>input_id_type=SCAFFOLD</font></p>
<p><br><font face="courier new,monospace">[Vertrna]<br>db=embl_vertrna<br>db_file=/usr/local/ensembl/embl_vertrna<br>program=tblastn<br>program_file=/usr/local/ensembl/programs/rmblast/bin/tblastn<br>parameters=-cpus => 1, -hitdist => 40<br>
module=BlastGenscanDNA<br>input_id_type=SCAFFOLD</font></p>
<div><br><font face="courier new,monospace">[Uniprot]<br>db=uniprot_sprot.fasta<br>db_file=/usr/local/ensembl/uniprot_sprot.fasta<br>program=blastp<br>program_file=/usr/local/ensembl/programs/rmblast/bin/blastp<br>parameters=-cpus => 1, -hitdist => 40<br>
module=BlastGenscanPep<br>input_id_type=SCAFFOLD</font></div>
<div><font face="Courier New"></font> </div>
<div><font face="Courier New"></font> </div>
<div><font face="Courier New">--------------------------------------------------------------------</font></div>
<div><font face="Courier New">rules.conf:</font></div>
<div><font face="Courier New"></font> </div>
<div><font face="Courier New">[Genscan]<br>condition=RepeatMask</font></div>
<div><font face="Courier New">[Eponine]<br>condition=SubmitScaffold</font></div>
<div><font face="Courier New">[UniGene]<br>condition=Genscan</font></div>
<div><font face="Courier New">[RepeatMask]<br>condition=SubmitScaffold</font></div>
<div><font face="Courier New">[Vertrna]<br>condition=Genscan</font></div>
<div><font face="Courier New">[Uniprot]<br>condition=Genscan</font></div>
<div><font face="Courier New">[TRF]<br>condition=SubmitScaffold</font></div>
<div><font face="Courier New"></font> </div>