Question: failure preparing job - workflow
0
gravatar for pwsmit
2.8 years ago by
pwsmit0
Netherlands
pwsmit0 wrote:

Hi, 

I managed to setup my own server (running on Ubuntu) and managed to perform the necessary analyses succesfully (i.e. no errors anymore and got the files I wanted WGS SNPs analyses). I converted it to a workflow and ran into various issues when I wanted to use the workflow, advice would be greatly appreciated! 

1. Reference FASTA file not selectable anymore with Realigner Target creator, Realigner, Mpileup, while Map with BWA can find the reference FASTA OK. did check the name and uploading as custom build did not help as I couldn't select the custom build. 

2. While FASTQC groomer and BWA runs OK, the function "Select on Data 6" I get: tool error; failure preparing job. when I rerun the failed history manually again (not changing anything) it runs OK but my workflow is stopped.  The error says: 

OperationalError: (OperationalError) database is locked u'UPDATE job SET update_time=?, command_line=? WHERE job.id = ?' ('2015-04-21 12:53:08.691793', "python /home/t4admin/galaxy/tools/filters/grep.py -i /home/t4admin/galaxy/database/files/000/dataset_142.dat -o /home/t4admin/galaxy/database/files/000/dataset_144.dat -pattern '^@' -v true", 118)

Anybody an idea what I am doing wrong?

Many thanks in advance, 

Pieter

 

workflow • 978 views
ADD COMMENTlink modified 2.8 years ago by Dannon Baker3.7k • written 2.8 years ago by pwsmit0
1
gravatar for Dannon Baker
2.8 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

Congrats on setting up your Galaxy server!  "Database is locked" happens sometimes with sqlite when multiple program threads are trying to access the database at the same time.  If this is a Galaxy server you intend to use for any serious analysis, I'd really recommend hooking it up to a postgres database and this problem won't happen anymore.  Here's our documentation on that:  https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_server

 

 

ADD COMMENTlink written 2.8 years ago by Dannon Baker3.7k
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