[ensembl-dev] Null submission ID

Diogo Costa costa.h4evr at gmail.com
Mon Mar 5 20:24:04 GMT 2012


Hi,

I'm having trouble running an analysis. Whatever pipeline step is
running, I'm getting "Null submission ID.." errors, such as:

FILE: EnsEMBL/Pipeline/Job.pm LINE: 396
CALLED BY: EnsEMBL/Pipeline/Job.pm  LINE: 492
Ensembl API version = 64
---------------------------------------------------
Job: Null submission ID for the following, but continuing: 91 92 94 95 97
98 100 101 103 104
Job: Null submission ID for the following, but continuing: 91 92 94 95 97
98 100 101 103 104
Job: Null submission ID for the following, but continuing: 91 92 94 95 97
98 100 101 103 104
Job: Null submission ID for the following, but continuing: 91 92 94 95 97
98 100 101 103 104
Job: Null submission ID for the following, but continuing: 91 92 94 95 97
98 100 101 103 104
Job: Null submission ID for the following, but continuing: 91 92 94 95 97
98 100 101 103 104
Job: Null submission ID for the following, but continuing: 91 92 94 95 97
98 100 101 103 104
Job: Null submission ID for the following, but continuing: 91 92 94 95 97
98 100 101 103 104
Job: Null submission ID for the following, but continuing: 91 92 94 95 97
98 100 101 103 104
Job: Null submission ID for the following, but continuing: 91 92 94 95 97
98 100 101 103 104
 I'm guessing there is something wrong with the way I create the input
id's, so here are the commands I run:

./analysis_setup.pl -dbhost localhost -dbuser ensembl
-dbpass ************** -dbname drosophila_americana_h5_core_64 -read -file
/usr/local/ensembl/genebuild/configs/analysis.conf

./rule_setup.pl  -dbhost localhost -dbuser ensembl -dbpass ************
-dbname drosophila_americana_h5_core_64 -read -file
/usr/local/ensembl/genebuild/configs/rules.conf

./make_input_ids -dbhost localhost -dbuser ensembl -dbpass ****** -dbname
drosophila_americana_h5_core_64 -slice -seq_level -coord_system scaffold
-logic_name SubmitScaffold

nohup ./rulemanager.pl -dbhost localhost -dbuser ensembl -dbpass *********
-dbname drosophila_americana_h5_core_64 &

The analysis and rules configurations are below.

The database has two coordinate systems: scaffold and chunk.

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 :\

Could you please help me?

Thank you,
Diogo Costa

Analysis.conf

[Eponine]
db=eponine
program=eponine-scan
program_file=/usr/bin/java
parameters=-epojar => /usr/local/ensembl/programs/eponine/eponine-scan.jar,
-threshold => 0.999
module=EponineTSS
input_id_type=SCAFFOLD

[RepeatMask]
db=repbase
db_version=20090604
db_file=repbase
program=RepeatMasker
program_version=open-3.3.0
program_file=/usr/local/ensembl/programs/RepeatMasker/RepeatMasker
parameters=-nolow -species "drosophila virilis" -s
module=RepeatMasker
gff_source=RepeatMask
gff_feature=repeat
input_id_type=SCAFFOLD

[SubmitScaffold]
input_id_type=SCAFFOLD
module=Dummy

[UniGene]
db=Dm_seq_all.fasta
db_file=/usr/local/ensembl/unigene/Dm_seq_all.fasta
program=tblastn
program_file=/usr/local/ensembl/programs/rmblast/bin/tblastn
parameters=-cpus => 1, -hitdist => 40
module=BlastGenscanDNA
input_id_type=SCAFFOLD


[Genscan]
db=/usr/local/ensembl/programs/genscan/HumanIso.smat
db_file=/usr/local/ensembl/programs/genscan/HumanIso.smat
program_file=genscan
module=Genscan
input_id_type=SCAFFOLD


[TRF]
program_file=/usr/local/ensembl/programs/trf/trf
module=TRF
input_id_type=SCAFFOLD


[Vertrna]
db=embl_vertrna
db_file=/usr/local/ensembl/embl_vertrna
program=tblastn
program_file=/usr/local/ensembl/programs/rmblast/bin/tblastn
parameters=-cpus => 1, -hitdist => 40
module=BlastGenscanDNA
input_id_type=SCAFFOLD

[Uniprot]
db=uniprot_sprot.fasta
db_file=/usr/local/ensembl/uniprot_sprot.fasta
program=blastp
program_file=/usr/local/ensembl/programs/rmblast/bin/blastp
parameters=-cpus => 1, -hitdist => 40
module=BlastGenscanPep
input_id_type=SCAFFOLD


--------------------------------------------------------------------
rules.conf:

[Genscan]
condition=RepeatMask
[Eponine]
condition=SubmitScaffold
[UniGene]
condition=Genscan
[RepeatMask]
condition=SubmitScaffold
[Vertrna]
condition=Genscan
[Uniprot]
condition=Genscan
[TRF]
condition=SubmitScaffold
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