Re: [galaxy-dev] Strange "Could not moveŠ." error

[Scott McManus]

Ok - that makes sense. So the from_work_dir attribute is part of the tool's 
 element under , 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
> > /h

Re: [galaxy-dev] Strange "Could not moveŠ." error

[Iry Witham]

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 mailto:scottmcma...@gatech.edu>>
Date: Thursday, August 2, 2012 12:59 PM
To: Iry Witham mailto:iry.wit...@jax.org>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto: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
galax

Re: [galaxy-dev] Strange "Could not moveŠ." error

[Jeremy Goecks]

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/d

Re: [galaxy-dev] Strange "Could not moveŠ." error

[Scott McManus]

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-