Hello,
I am setting up a local galaxy installation and using our local SGE
cluster to run the jobs as real users.
One of the first few tools I tested was the ncbi makebkastdb tool. When
I try to run it the history for that particular job is immediately shown
as follows:
0: (unnamed dataset)
Failed to retrieve dataset information.
An error occurred with this dataset:/hasattr(): attribute name must be
string/
In the stdout of the job I was getting the following error:
Fatal error: Matched on Error:
Error: NCBI C++ Exception:
"/usr/local/src/ncbiblast+/2.2.27/c++/src/objtools/blast/seqdb_writer/build_db.cpp",
line 979: Error: ncbi::s_CreateDirectories() - Failed to create directory
'dataset_38_files'
I finally figured out that the makedb wrapper was using
$outfile.extra_files_path instead of $outfile.files_path. I fixed the
wrapper and restarted the instance. The job now runs ok and reports
successful completion in the stdout.
But, the history for this particular job is still shown as explained above.
Can somebody help me figure out what is going wrong in my setup?
Here are some of the relevant logs:
==> web1.log <==
128.192.203.31 - - [19/Mar/2013:15:14:35 -0400] "POST /tool_runner/index
HTTP/1.1" 200 -
"http://galaxy.qbcg.uga.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.0.1";
"Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.22 (KHTML, like
Gecko) Chrome/25.0.1364.172 Safari/537.22"
==> web0.log <==
128.192.203.31 - - [19/Mar/2013:15:14:36 -0400] "GET /history HTTP/1.1"
200 - "http://galaxy.qbcg.uga.edu/tool_runner/index"; "Mozilla/5.0
(Windows NT 6.1; WOW64) AppleWebKit/537.22 (KHTML, like Gecko)
Chrome/25.0.1364.172 Safari/537.22"
galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,161
Error in history API at listing contents with history d413a19dec13d11e,
hda e89067bb68bee7a0: hasattr(): attribute name must be string
galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,316
Error in history API at listing contents with history d413a19dec13d11e,
hda ba03619785539f8c: hasattr(): attribute name must be string
galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,316
Error in history API at listing contents with history d413a19dec13d11e,
hda cbbbf59e8f08c98c: hasattr(): attribute name must be string
galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,317
Error in history API at listing contents with history d413a19dec13d11e,
hda 964b37715ec9bd22: hasattr(): attribute name must be string
galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,317
Error in history API at listing contents with history d413a19dec13d11e,
hda 1fad1eaf5f4f1766: hasattr(): attribute name must be string
galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,318
Error in history API at listing contents with history d413a19dec13d11e,
hda 2fdbd5c5858e78fb: hasattr(): attribute name must be string
==> manager.log <==
galaxy.jobs.manager DEBUG 2013-03-19 15:14:40,856 (42) Job assigned to
handler 'handler0'
==> handler0.log <==
galaxy.jobs DEBUG 2013-03-19 15:14:41,790 (42) Working directory for job
is:
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42
galaxy.jobs.rules.200_rules DEBUG 2013-03-19 15:14:41,791
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.0.1
galaxy.jobs.handler DEBUG 2013-03-19 15:14:41,792 dispatching job 42 to
drmaa runner
galaxy.jobs.handler INFO 2013-03-19 15:14:41,882 (42) Job dispatched
galaxy.tools DEBUG 2013-03-19 15:14:42,068 Building dependency shell
command for dependency 'makeblastdb'
galaxy.tools WARNING 2013-03-19 15:14:42,068 Failed to resolve
dependency on 'makeblastdb', ignoring
galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:42,453 (42) submitting
file
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/pbs/galaxy_42.sh
galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:42,453 (42) command is:
makeblastdb -version &>
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_42;
makeblastdb -out
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/dataset_41_files/blastdb
-hash_index -in "
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/files/000/dataset_30.dat
" -title "wert" -dbtype nucl; cd
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist;
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/set_metadata.sh
./database/files
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42
.
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/universe_wsgi.ini
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/tmp/tmpxi116L
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/galaxy.json
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/metadata_in_HistoryDatasetAssociation_40_4YjnIJ,/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/metadata_kwds_HistoryDatasetAssociation_40_fWHejS,/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/metadata_out_HistoryDatasetAssociation_40_BwBD1y,/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/metadata_results_HistoryDatasetAssociation_40_0IjMAn,/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/galaxy_dataset_41.dat,/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/metadata_override_HistoryDatasetAssociation_40_pXhQCd
galaxy.jobs DEBUG 2013-03-19 15:14:42,456 (42) Changing ownership of
working directory with: /usr/bin/sudo -E
scripts/external_chown_script.py
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42
raj76 1083
galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:42,766 (42) submitting
with credentials: raj76 [uid: 740]
galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:42,774 (42) Job script
for external submission is:
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/pbs/42.jt_json
galaxy.jobs.runners.drmaa INFO 2013-03-19 15:14:43,198 (42) queued as
2246095
galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:43,420 (42/2246095)
state change: job is queued and active
galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:54,444 (42/2246095)
state change: job is running
galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:15:04,614 (42/2246095) job
left DRM queue with following message: code 18: The job specified by the
'jobid' does not exist.
galaxy.jobs DEBUG 2013-03-19 15:15:04,648 (42) Changing ownership of
working directory with: /usr/bin/sudo -E
scripts/external_chown_script.py
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42
galaxy 1234
galaxy.jobs DEBUG 2013-03-19 15:15:06,988 (42) Changing ownership of
working directory with: /usr/bin/sudo -E
scripts/external_chown_script.py
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42
galaxy 1234
galaxy.jobs DEBUG 2013-03-19 15:15:07,833 finish(): Moved
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/galaxy_dataset_41.dat
to
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/files/000/dataset_41.dat
galaxy.tools DEBUG 2013-03-19 15:15:09,546 Error opening galaxy.json
file: [Errno 2] No such file or directory:
'/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/galaxy.json'
galaxy.jobs DEBUG 2013-03-19 15:15:09,626 job 42 ended
galaxy.datatypes.metadata DEBUG 2013-03-19 15:15:09,626 Cleaning up
external metadata files
galaxy.objectstore CRITICAL 2013-03-19 15:15:09,665
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42
delete error [Errno 39] Directory not empty:
'/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42'
==> web1.log <==
sqlalchemy.pool.QueuePool.0x...4350 WARNING 2013-03-19 15:16:14,801
Error closing cursor: current transaction is aborted, commands ignored
until end of transaction block
Thanks,
-Raj
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