Question: (Closed) Local Galaxy with grey process
0
gravatar for jardim.rodrigo
10 months ago by
Brazil / Rio de Janeiro / Fiocruz
jardim.rodrigo10 wrote:

Hi all,

I have a local galaxy installed and today I try submit Bowtie2 process and in my history the entry just stay in grey state. In galaxy log I have the message below but the process stay in grey state. Any ideas? Thanks!

galaxy.tools DEBUG 2017-01-25 15:25:33,806 Validated and populated state for tool request (123.974 ms) galaxy.tools.actions INFO 2017-01-25 15:25:33,900 Handled output named output for tool toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2 (32.987 ms) galaxy.tools.actions INFO 2017-01-25 15:25:33,909 Added output datasets to history (7.924 ms) galaxy.tools.actions INFO 2017-01-25 15:25:33,971 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2] (46.832 ms) galaxy.tools.actions INFO 2017-01-25 15:25:33,973 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2] complete, ready to flush (64.373 ms) galaxy.tools.actions INFO 2017-01-25 15:25:34,009 Flushed transaction for job Job[id=11524,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2] (35.955 ms) galaxy.tools.execute DEBUG 2017-01-25 15:25:34,009 Tool [toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2] created job [11524] (160.242 ms) galaxy.tools.execute DEBUG 2017-01-25 15:25:34,023 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2 request: (216.554 ms)

galaxy • 256 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by jardim.rodrigo10

This may sound simple to try, but have you refreshed the History panel (double circle icon, top of right panel)? This updates the job states (appears that job ran, from the log).

ADD REPLYlink written 10 months ago by Jennifer Hillman Jackson23k

Hi Jennifer thanks for your answer, but is not the problem. I'm trying reinstall all tools with this problem. Thank you.

ADD REPLYlink written 10 months ago by jardim.rodrigo10

Hi all!

My problem persists. Today I reinstalled all the tools that had problems, but it was not solved. So I looked at the log file and found that Galaxy does not call galaxy.jobs. In these tools, the log stops at galaxy.tools.execute. When the tool is working properly, the log file displays rows with galaxy.jobs, galaxy.jobs.handler, galaxy.tools.deps, galaxy.jobs.command_factory, and so on.

Please, any idea? Thanks all!

ADD REPLYlink written 10 months ago by jardim.rodrigo10
1
gravatar for jardim.rodrigo
10 months ago by
Brazil / Rio de Janeiro / Fiocruz
jardim.rodrigo10 wrote:

Hi. I solved! The problem was with database model. I updated my local galaxy release and the database model was not updated correctly. I had migrate the database model "on the nail" ;)

Thanks!

ADD COMMENTlink written 10 months ago by jardim.rodrigo10

Thanks for posting back and glad the problem is resolved! Jen

ADD REPLYlink written 10 months ago by Jennifer Hillman Jackson23k
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