[ensembl-dev] missing job information in pipeline run

江文恺 jiangwenkai at mail.kib.ac.cn
Sat Oct 23 09:07:24 BST 2010

Hi, all
recently i update my api into ensembl59, also update the pipeline and analysis code to most recent status.
however, i encounter a strange problem, 
when i run the pipeline with rulemanager, the pipeline runs well, but the job information are totally missing from the mysql database tables, both job table and job_status table, and the input_id_analysis_table does not record the succefully running input_ids.
eg: after successfully run RepeatMask:
mysql> select * from input_id_analysis where analysis_id=2; (2 is for RepeatMask analysis)
Empty set (0.00 sec)

so i check through monitor script, but found that all informations seems to be right, although missing in the job/job_status table .

jiangwenkai at node69:~/ensembl/tmp/> perl ~/ensembl/ensembl-pipeline/scripts/monitor -dbuser jwk -dbpass jwk -dbhost node69 -dbport 3307 -dbname oryza_glaberrima_core_6_59_1 -finishedpercent

Finished job summary [node69:3307 oryza_glaberrima_core_6_59_1]

Count  Name               Id%Done
-----  ----               -------
15858  Submitsupercontig  1  100%
15858  RepeatMask         2  100%
12030  TRF                4   75%

any ideas?

the running parameters is 
rulemanager "mysqldb args" -verbose -force_accumulators -input_id_type XXX -analysis XXX
configuration for job submit looks like: 
bacth size =1,
runner = /ensembl-pipeline/Bio/EnsEMBL/Pipeline/runner.pl
cleanup= no
verbose= warning

Thanks for all


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