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 The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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 The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Scott, I am running SUSE Linux Enterprise Server 11 SP1 (x86_64) - Kernel \r (\l) on both servers. These are VM's with identical configurations. I know that shutil.move is a python function, but I am not really sure how it works. I appreciate the assistance. Iry From: Scott McManus <scottmcmanus@gatech.edu<mailto:scottmcmanus@gatech.edu>> Date: Thursday, August 2, 2012 12:59 PM To: Iry Witham <iry.witham@jax.org<mailto:iry.witham@jax.org>> Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" <galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>> Subject: Re: [galaxy-dev] Strange "Could not moveŠ." error 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 ________________________________ 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 The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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 The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Ok - that makes sense. So the from_work_dir attribute is part of the tool's <data> element under <outputs>, and Jeremy fixed a timing issue. Thanks, Jeremy! -Scott ----- Original Message -----
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
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Iry Witham -
Jeremy Goecks -
Scott McManus