Hi Iry-
A call to shutil.move is failing, and this could be because file-copying
semantics
are different on your test instance's OS and/or filesystem than they are on
your
development instance's OS and/or filesystem. What OS and file system are you
using on each? We can also try writing a small Python script to see if
shutil.move
is failing when copying files from a similar source directory to a similar
destination
directory. Let me know and I'll be glad to give you a hand.
-Scott
----- Original Message -----
> 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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