On Wed, Jan 11, 2012 at 11:16 AM, Nate Coraor <n...@bx.psu.edu> wrote:

> On Jan 11, 2012, at 10:56 AM, Ryan Golhar wrote:
>
> > it is also set to True:
> > > [galaxy@bic galaxy-dist]$ grep Ryan *.log
> > > runner0.log:galaxy.jobs WARNING 2012-01-10 22:17:26,381 Ryan Golhar -
> self.set_metadata_externally = True
> > >
> > > Clearly something else is going on here.  On my last import of BAM
> file, even after samtools finished indexing the BAM files, Galaxy never
> registered those jobs as completed.  So this problem is still there as well.
> >
> > Thanks for checking these.  So, what does your server log for runner0
> look like?
> >
> >
> > > it is also set to True:
> > > [galaxy@bic galaxy-dist]$ grep Ryan *.log
> > > runner0.log:galaxy.jobs WARNING 2012-01-10 22:17:26,381 Ryan Golhar -
> self.set_metadata_externally = True
>
> Sorry, I should have been more specific.  What are the contents of the log
> from job start to finish?
>
> --nate
>
> >
>
> I think this is it.  The rest looks like stuff for jobs I started today.
 I wonder if Galaxy is running the jobs on the head node because its unable
to change the permissions of the BAM files.  The BAM files are located on a
read-only NFS mount.

serving on http://127.0.0.1:8079
galaxy.jobs DEBUG 2012-01-10 22:16:54,322 dispatching job 62 to pbs runner
galaxy.jobs INFO 2012-01-10 22:16:54,436 job 62 dispatched
galaxy.jobs.runners.pbs DEBUG 2012-01-10 22:16:54,595 (62) submitting file
/home/galaxy/galaxy-dist-9/database/pbs/62.sh
galaxy.jobs.runners.pbs DEBUG 2012-01-10 22:16:54,596 (62) command is:
python /home/galaxy/galaxy-dist-9/tools/data_source/upload.py
/home/galaxy/galaxy-dist-9 /home/galaxy/galaxy-dist-9/datatypes_conf.xml
/home/galaxy/galaxy-dist-9/database/tmp/tmpaEn2
jR
181:/home/galaxy/galaxy-dist-9/database/job_working_directory/62/dataset_181_files:None

182:/home/galaxy/galaxy-dist-9/database/job_working_directory/62/dataset_182_files:None
        183:/home/galaxy/galaxy-dist-9/database/job_workin
g_directory/62/dataset_183_files:None
184:/home/galaxy/galaxy-dist-9/database/job_working_directory/62/dataset_184_files:None;
cd /home/galaxy/galaxy-dist-9; /home/galaxy/galaxy-dist-9/set_metadata.sh
./database/files ./database/tmp . datatypes_
conf.xml ./database/job_working_directory/62/galaxy.json
galaxy.jobs.runners.pbs DEBUG 2012-01-10 22:16:54,597 (62) queued in
default queue as 73.localhost.localdomain
galaxy.jobs.runners.pbs DEBUG 2012-01-10 22:16:55,179
(62/73.localhost.localdomain) PBS job state changed from N to R
galaxy.jobs.runners.pbs DEBUG 2012-01-10 22:17:26,324
(62/73.localhost.localdomain) PBS job state changed from R to C
galaxy.jobs.runners.pbs DEBUG 2012-01-10 22:17:26,324
(62/73.localhost.localdomain) PBS job has completed successfully
galaxy.jobs WARNING 2012-01-10 22:17:26,381 Ryan Golhar -
self.set_metadata_externally = True
galaxy.jobs WARNING 2012-01-11 01:29:53,110 Ryan Golhar -
self.set_metadata_externally = True
galaxy.jobs WARNING 2012-01-11 04:30:06,043 Ryan Golhar -
self.set_metadata_externally = True
galaxy.jobs WARNING 2012-01-11 07:41:02,917 Ryan Golhar -
self.set_metadata_externally = True
galaxy.util WARNING 2012-01-11 10:22:40,046 Unable to honor umask (02) for
/mnt/isilon/cag/ngs/hiseq/golharr/Bookman/5500xl_5_2011_BK_WTS_03_122211_1_06-2-1.bam,
tried to set: 0664 but mode remains 0771, error was: [Errno 30] Read-only
file system: '/mn
t/isilon/cag/ngs/hiseq/golharr/Bk/5500xl_5_2011_BK_WTS_03_122211_1_06-2-1.bam'
galaxy.util WARNING 2012-01-11 10:22:40,066 Unable to honor primary group
(grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=503, gr_mem=[]))
for
/mnt/isilon/cag/ngs/hiseq/golharr/Bookman/5500xl_5_2011_BK_WTS_03_122211_1_06-2-1.bam,
group remains
 grp.struct_group(gr_name='cag_lab2', gr_passwd='x', gr_gid=10726,
gr_mem=['ryang', 'lifeng', 'galaxy']), error was: [Errno 30] Read-only file
system:
'/mnt/isilon/cag/ngs/hiseq/golharr/Bk/5500xl_5_2011_BK_WTS_03_122211_1_06-2-1.bam'
galaxy.util WARNING 2012-01-11 10:22:40,069 Unable to honor umask (02) for
/mnt/isilon/cag/ngs/hiseq/golharr/Bookman/5500_4_BK_WTS_03_20111222_1_04-1-1.bam,
tried to set: 0664 but mode remains 0771, error was: [Errno 30] Read-only
file system: '/mnt/isi
lon/cag/ngs/hiseq/golharr/Bk/5500_4_BK_WTS_03_20111222_1_04-1-1.bam'
galaxy.util WARNING 2012-01-11 10:22:40,069 Unable to honor primary group
(grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=503, gr_mem=[]))
for
/mnt/isilon/cag/ngs/hiseq/golharr/Bk/5500_4_BK_WTS_03_20111222_1_04-1-1.bam,
group remains grp.
struct_group(gr_name='cag_lab2', gr_passwd='x', gr_gid=10726,
gr_mem=['ryang', 'lifeng', 'galaxy']), error was: [Errno 30] Read-only file
system:
'/mnt/isilon/cag/ngs/hiseq/golharr/Bk/5500_4_BK_WTS_03_20111222_1_04-1-1.bam'
galaxy.util WARNING 2012-01-11 10:22:40,072 Unable to honor umask (02) for
/mnt/isilon/cag/ngs/hiseq/golharr/Bk/5500xl_5_2011_BK_WTS_03_122211_1_04-1-1.bam,
tried to set: 0664 but mode remains 0771, error was: [Errno 30] Read-only
file system: '/mn
t/isilon/cag/ngs/hiseq/golharr/Bk/5500xl_5_2011_BK_WTS_03_122211_1_04-1-1.bam'
galaxy.util WARNING 2012-01-11 10:22:40,072 Unable to honor primary group
(grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=503, gr_mem=[]))
for
/mnt/isilon/cag/ngs/hiseq/golharr/Bk/5500xl_5_2011_BK_WTS_03_122211_1_04-1-1.bam,
group remains
 grp.struct_group(gr_name='cag_lab2', gr_passwd='x', gr_gid=10726,
gr_mem=['ryang', 'lifeng', 'galaxy']), error was: [Errno 30] Read-only file
system:
'/mnt/isilon/cag/ngs/hiseq/golharr/Bk/5500xl_5_2011_BK_WTS_03_122211_1_04-1-1.bam'
galaxy.util WARNING 2012-01-11 10:22:40,072 Unable to honor umask (02) for
/mnt/isilon/cag/ngs/hiseq/golharr/Bookman/5500_4_BK_WTS_03_20111222_1_06-2-1.bam,
tried to set: 0664 but mode remains 0771, error was: [Errno 30] Read-only
file system: '/mnt/isi
lon/cag/ngs/hiseq/golharr/Bk/5500_4_BK_WTS_03_20111222_1_06-2-1.bam'
galaxy.util WARNING 2012-01-11 10:22:40,072 Unable to honor primary group
(grp.struct_group(gr_name='galaxy', gr_passwd='x', gr_gid=503, gr_mem=[]))
for
/mnt/isilon/cag/ngs/hiseq/golharr/Bk/5500_4_BK_WTS_03_20111222_1_06-2-1.bam,
group remains grp.
struct_group(gr_name='cag_lab2', gr_passwd='x', gr_gid=10726,
gr_mem=['ryang', 'lifeng', 'galaxy']), error was: [Errno 30] Read-only file
system:
'/mnt/isilon/cag/ngs/hiseq/golharr/Bk/5500_4_BK_WTS_03_20111222_1_06-2-1.bam'
galaxy.jobs DEBUG 2012-01-11 10:22:40,161 job 62 ended
galaxy.datatypes.metadata DEBUG 2012-01-11 10:22:40,162 Cleaning up
external metadata files
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