[ensembl-dev] ensembl-funcgen SubmitPeaks error
Lel Eory
lel.eory at roslin.ed.ac.uk
Tue May 20 15:03:12 BST 2014
Dear All,
I try to run some ChIP-seq analyses with the ensembl-functgenomics
pipeline (version 72) using ensembl-hive (version lg4_pre_rel72_20130423).
In the efg sequencing environment I have added the peak datasets with
AddPeakDataSets and try to run beekeeper.pl to set-up the peak analysis
pipelines.
But the setup_pipeline step fails with the following (full beekeeper.pl
output is at the end of this e-mail):
beekeeper.pl -url $DBURL/leory2_peaks_lel_sus_scrofa_funcgen_72_102
-hive_log_dir hive_log_dir -run
~~~~~~~~~~~~~~~~~~~~~~~~~~
Storing new InputSet: piPSC_H3K27me3_Xiao
DBD::mysql::st execute failed: Column 'replicate' cannot be null at
/groups2/avian_genomes/software/src/ensembl/ens72/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/InputSetAdaptor.pm
line 380.
job 1 : died in status 'RUN' for the following reason: DBD::mysql::st
execute failed: Column 'replicate' cannot be null at
/groups2/avian_genomes/software/src/ensembl/ens72/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/InputSetAdaptor.pm
line 380.
~~~~~~~~~~~~~~~~~~~~~~~~~~
Where should I specify the number of replicates (in this case it is just
1) for setup_pipeline within the peak analysis step or where does
setup-pipeline get this value from?
Thank you.
Kind regards,
Lel
beekeeper.pl -url $DBURL/leory2_peaks_lel_sus_scrofa_funcgen_72_102
-hive_log_dir hive_log_dir -run
~~~~~~~~~~~~~ beekeeper.pl output ~~~~~~~~~~~~~
======= beekeeper loop ** 1 **==========
GarbageCollector: Checking for lost Workers...
GarbageCollector: [Queen:] we have 0 Workers alive.
setup_pipeline ( 1) LOADING jobs(Sem:0, Rdy:3,
InProg:0, Done+Pass:0, Fail:0)=3 Ave_msec:0, workers(Running:0,
Reqired:0) h.cap:1 a.cap:- (sync'd 1400493652 sec ago)
run_peaks ( 2) EMPTY jobs(Sem:0, Rdy:0,
InProg:0, Done+Pass:0, Fail:0)=0 Ave_msec:0, workers(Running:0,
Reqired:0) h.cap:10 a.cap:- (sync'd 1400493652 sec ago)
run_peaks_wide ( 3) EMPTY jobs(Sem:0, Rdy:0,
InProg:0, Done+Pass:0, Fail:0)=0 Ave_msec:0, workers(Running:0,
Reqired:0) h.cap:10 a.cap:- (sync'd 1400493652 sec ago)
run_macs ( 4) EMPTY jobs(Sem:0, Rdy:0,
InProg:0, Done+Pass:0, Fail:0)=0 Ave_msec:0, workers(Running:0,
Reqired:0) h.cap:10 a.cap:- (sync'd 1400493652 sec ago)
===== Stats of live Workers according to the Queen: ======
======= TOTAL ======= : 0 workers
setup_pipeline ( 1) READY jobs(Sem:0, Rdy:3,
InProg:0, Done+Pass:0, Fail:0)=3 Ave_msec:0, workers(Running:0,
Reqired:3) h.cap:1 a.cap:- (sync'd 0 sec ago)
Before checking the Valley for pending jobs, Scheduler allocated
1 x LOCAL:default extra workers for 'setup_pipeline' [0.0000 hive_load
remaining]
Scheduler is going to submit 1 x LOCAL:default workers
Submitting 1 workers (rc_name=default) to LOCAL/ris-lx10
SUBMITTING_CMD: runWorker.pl -url
'$DBURL/leory2_peaks_lel_sus_scrofa_funcgen_72_102' -rc_name default &
hive 0.000% complete (< 0.000 CPU_hrs) (3 todo + 0 done + 0
failed = 3 total)
The Beekeeper has stopped because the number of loops was limited
by 1 and this limit expired
dbc 0 disconnect cycles
Queen picked analysis with dbID=1 for the worker
Worker: meadow=LOCAL/ris-lx10,
process=35314 at ris-lx10.roslin.ed.ac.uk, resource_class_id=1,
last_check_in=2014-05-19 11:00:52, analysis=setup_pipeline(1)
batch_size = 1
life_span = 3600
worker_log_dir = STDOUT/STDERR
Setting name at
/groups2/avian_genomes/software/src/ensembl/ens72/ensembl/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
line 344.
:: Auto-selecting build 102 core DB as:
anonymous at sus_scrofa_core_75_102:ensembldb.ensembl.org:5306
ParamWarning: value for param('set_name') is used before having
been initialized!
ParamWarning: value for param('group') is used before having been
initialized!
ParamWarning: value for param('input_dir') is used before having
been initialized!
ParamWarning: value for param('data_file') is used before having
been initialized!
------------------ DEPRECATED ---------------------
Deprecated method call in file
/groups2/avian_genomes/software/src/ensembl/ens72/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/RunnableDB/SetupPeaksPipeline.pm
line 41.
Method
Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor::fetch_group_details is deprecated.
Please use ExperimentalGroupAdaptor
Ensembl API version = 72
---------------------------------------------------
Preprocess cmd: gzip -dc
/groups2/pig_project/ensembl_funcgen/xiao_chip_seq/alignments/sus_scrofa/Sscrofa10.2/Xiao/piPSC_Pig-IgG_Xiao.samse.sam.gz
| grep -vE
'^[^[:space:]]+[[:blank:]][^[:space:]]+[[:blank:]][^[:space:]]+:[^[:space:]]+:MT:'
| grep -v '^MT' | grep -v '^chrM' |
/groups2/avian_genomes/software/bin/ensembl-funcgen/samtools view -uSh
-t
/groups2/pig_project/ensembl_funcgen/xiao_chip_seq/sam_header/sus_scrofa/sus_scrofa_male_Sscrofa10.2_unmasked.fasta.fai
-F 4 - | /groups2/avian_genomes/software/bin/ensembl-funcgen/samtools
sort -
/groups2/pig_project/ensembl_funcgen/xiao_chip_seq/alignments/sus_scrofa/Sscrofa10.2/Xiao/piPSC_Pig-IgG_Xiao.samse.sam.gz_tmp
; /groups2/avian_genomes/software/bin/ensembl-funcgen/samtools rmdup -s
/groups2/pig_project/ensembl_funcgen/xiao_chip_seq/alignments/sus_scrofa/Sscrofa10.2/Xiao/piPSC_Pig-IgG_Xiao.samse.sam.gz_tmp.bam
- | /groups2/avian_genomes/software/bin/ensembl-funcgen/samtools view -h
- | gzip -c >
/groups2/pig_project/ensembl_funcgen/xiao_chip_seq/output/lel_sus_scrofa_funcgen_72_102/peaks/results/Xiao/piPSC_Pig-IgG_Xiao.samse.sam.gz
; rm -f
/groups2/pig_project/ensembl_funcgen/xiao_chip_seq/alignments/sus_scrofa/Sscrofa10.2/Xiao/piPSC_Pig-IgG_Xiao.samse.sam.gz_tmp.bam
Storing new InputSet: piPSC_H3K27me3_Xiao
DBD::mysql::st execute failed: Column 'replicate' cannot be null
at
/groups2/avian_genomes/software/src/ensembl/ens72/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/InputSetAdaptor.pm
line 380.
job 1 : died in status 'RUN' for the following reason:
DBD::mysql::st execute failed: Column 'replicate' cannot be null at
/groups2/avian_genomes/software/src/ensembl/ens72/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/InputSetAdaptor.pm
line 380.
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