Iry,

This is probably an issue with using the from_work_dir attribute. 

Prior to changeset 524cfb8ca67d, the attribute didn't work when 
set_metadata_externally was True; 524cfb8ca67d modified the attribute 
implementation so that it works regardless of how metadata is set. This 
changeset is not in the most recent distribution, so you'll need to pull from 
-central if you want to use it immediately.

Best,
J.


On Aug 2, 2012, at 12:24 PM, Iry Witham wrote:

> Hi Dev-Team,
> 
> I am experiencing a strange error that I cannot replicate on two identical 
> instances of my Galaxy server.  I have a tool that runs fine on my test 
> instance and fails on my development instance.  The servers are identically 
> configured and running the same build.  The handler.log from the successful 
> instance shows the following:
> 
> galaxy.jobs DEBUG 2012-08-02 11:31:07,881 (295) Working directory for job is: 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295
> galaxy.jobs.handler DEBUG 2012-08-02 11:31:07,881 dispatching job 295 to pbs 
> runner
> galaxy.jobs.handler INFO 2012-08-02 11:31:08,083 (295) Job dispatched
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) submitting file 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/pbs/295.sh
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) command is: perl 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl        
>  --out-basename cnv_seq_result         --test 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1504.dat
>              --ref 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1503.dat
>              --genome-size 2716965481         --p-value 0.001         
> --bigger-window 1.5             --no-annotate             --log2-threshold 
> 0.6; cd /hpcdata/galaxy-test/galaxy-setup/galaxy-dist; 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/set_metadata.sh 
> ./database/files 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295
>  . /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmplTSKeF 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/galaxy.json
>  
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_in_HistoryDatasetAssociation_689_Oh21hx,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_kwds_HistoryDatasetAssociation_689_xgxlZy,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_out_HistoryDatasetAssociation_689_H0claK,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_results_HistoryDatasetAssociation_689_rdQBs8,,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_override_HistoryDatasetAssociation_689_B0U0MV
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,395 (295) queued in default 
> queue as 112605.scyld.localdomain
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,776 
> (295/112605.scyld.localdomain) PBS job state changed from N to R
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,117 
> (295/112605.scyld.localdomain) PBS job state changed from R to C
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,118 
> (295/112605.scyld.localdomain) PBS job has completed successfully
> galaxy.jobs DEBUG 2012-08-02 11:31:27,197 finish(): Moved 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/cnv_seq_result.cnv
>  to 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1555.dat
>  as directed by from_work_dir
> galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,249 loading metadata from 
> file for: HistoryDatasetAssociation 689
> galaxy.jobs DEBUG 2012-08-02 11:31:27,382 job 295 ended
> galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,382 Cleaning up external 
> metadata files
> 
> The same log from the failing instance shows the following:
> 
> galaxy.jobs DEBUG 2012-08-02 11:54:29,234 (113) Working directory for job is: 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113
> galaxy.jobs.handler DEBUG 2012-08-02 11:54:29,234 dispatching job 113 to pbs 
> runner
> galaxy.jobs.handler INFO 2012-08-02 11:54:29,420 (113) Job dispatched
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) submitting file 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/pbs/113.sh
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) command is: perl 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl         
> --out-basename cnv_seq_result         --test 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_131.dat
>              --ref 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_132.dat
>              --genome-size 2716965481         --p-value 0.001         
> --bigger-window 1.5             --no-annotate             --log2-threshold 
> 0.6; cd /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist; 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113
>  . /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/universe_wsgi.ini 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/tmp/tmpgTn7ey 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/galaxy.json
>  
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_in_HistoryDatasetAssociation_136_VYG968,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_kwds_HistoryDatasetAssociation_136_yo_4aK,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_out_HistoryDatasetAssociation_136_D6HwmI,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_results_HistoryDatasetAssociation_136_zunslF,,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_override_HistoryDatasetAssociation_136_FDUxso
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,680 (113) queued in default 
> queue as 112609.scyld.localdomain
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:30,163 
> (113/112609.scyld.localdomain) PBS job state changed from N to R
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:33,298 
> (113/112609.scyld.localdomain) PBS job state changed from R to C
> galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:33,298 
> (113/112609.scyld.localdomain) PBS job has completed successfully
> galaxy.jobs DEBUG 2012-08-02 11:54:33,354 finish(): Could not move 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/cnv_seq_result.cnv
>  to 
> /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_140.dat
>  as directed by from_work_dir
> galaxy.jobs DEBUG 2012-08-02 11:54:33,467 job 113 ended
> 
> Why would one fail and the other succeed? 
> 
> Thanks,
> Iry
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