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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