Improve Moa error logging for ruff jobs
Reported by john.mccallum (at plantandfood) | May 25th, 2011 @ 01:08 AM | in v1.1
[cfljam@pgenome 15.BLASTX_USDA_GH32]$ pwd
/data/moa/onion/70.CG_marker_design/40.CHO/GH32/15.BLASTX_USDA_GH32
[cfljam@pgenome 15.BLASTX_USDA_GH32]$ moa show db
/data/moa/db/uniprot/10.uniprot.trembl/uniprot_trembl
eval 1e-10
gff_blasthit F
gff_source BLAST
input ../12.retrieve_USDA_GH32/.fasta
nohits 50
nothreads 2
outgff gff/.gff
output out/*.out
postcommand
precommand
program blastx
project
title Blast against Trembl PLants
[cfljam@pgenome 15.BLASTX_USDA_GH32]$ ls -l .. total 16
drwxrwxr-x 2 cfljam users 4096 May 24 13:27 00.raw_data_motifs
drwxrwxr-x 3 cfljam users 4096 May 25 12:51 11.fuzztran
drwxrwxr-x 3 cfljam users 4096 May 25 13:00
12.retrieve_USDA_GH32
drwxrwxr-x 5 cfljam users 4096 May 25 13:06 15.BLASTX_USDA_GH32
[cfljam@pgenome 15.BLASTX_USDA_GH32]$ ls -la total 20
drwxrwxr-x 5 cfljam users 4096 May 25 13:06 .
drwxrwxr-x 6 cfljam users 4096 May 25 13:02 ..
drwxrwxr-x 2 cfljam users 4096 May 25 13:06 gff
drwxrwxr-x 4 cfljam users 4096 May 25 13:07 .moa
drwxrwxr-x 2 cfljam users 4096 May 25 13:06 out
[cfljam@pgenome 15.BLASTX_USDA_GH32]$moa run
File "/opt/moa10/lib/python/moa/backend/ruff.py", line 381, in executor
raise ruffus.JobSignalledBreak
JobSignalledBreak:
Warning: Encountered a run error?
Traceback (most recent call last):
File "/opt/moa10/bin/moa", line 318, in
run_1()
File "/opt/moa10/bin/moa", line 292, in run_1
run_2()
File "/opt/moa10/bin/moa", line 246, in run_2
run_3(wd)
File "/opt/moa10/bin/moa", line 201, in run_3
silent = sysConf.options.silent)
File "/opt/moa10/lib/python/moa/job.py", line 250, in execute
execNow, verbose = verbose, silent=silent)
File "/opt/moa10/lib/python/moa/backend/ruff.py", line 241, in execute
logger = ruffus.black_hole_logger,
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 2680, in pipeline_run ruffus.ruffus_exceptions.RethrownJobError:
Exceptions running jobs for
'def moa.backend.ruff.executor(...):'
Original exception:
Exception [#1](/projects/73665/tickets/1 "Ticket #1")
ruffus.ruffus_exceptions.JobSignalledBreak(
):
for moa.backend.ruff.executor.Job = [[[../12.retrieve_USDA_GH32/5225.singletons_GH32.fasta, uniprot_trembl]] -> [gff/5225.singletons_GH32.gff, out/5225.singletons_GH32.out], #!/bin/bash -e
blastall -i ../12.retrieve_USDA_GH32/5225.singletons_GH32.fasta -p blastx \
-e 1e-10 -m 7 -a 2 -d /data/moa/db/uniprot/10.uniprot.trembl/uniprot_trembl \
-b 50 -v 50 -o out/5225.singletons_GH32.out
cat out/5225.singletons_GH32.out | blast2gff -b F \
-s BLAST -d query > gff/5225.singletons_GH32.gff, {'program': 'blastx', 'postcommand': '', 'wd': '/data/moa/onion/70.CG_marker_design/40.CHO/GH32/15.BLASTX_USDA_GH32', 'precommand': '', 'db': '/data/moa/db/uniprot/10.uniprot.trembl/uniprot_trembl', 'job': <moa.job.Job object at 0x10facf50>, 'nothreads': '2', 'eval': '1e-10', 'input': '../12.retrieve_USDA_GH32/5225.singletons_GH32.fasta', 'outgff': 'gff/5225.singletons_GH32.gff', 'silent': None, 'default_command': 'run', 'moa_filesets': ['input', 'db', 'outgff', 'output'], 'title': 'Blast against Trembl PLants', 'project': '', 'gff_source': 'BLAST', 'nohits': '50', 'gff_blasthit': 'F', 'output': 'out/5225.singletons_GH32.out'}]
Traceback (most recent call last):
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 517, in run_pooled_job_without_exceptions
return_value = job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 447, in job_wrapper_io_files
ret_val = user_defined_work_func(*param)
File "/opt/moa10/lib/python/moa/backend/ruff.py", line 381, in executor
raise ruffus.JobSignalledBreak
JobSignalledBreak:
Comments and changes to this ticket
-
MF May 31st, 2011 @ 09:11 PM
- Tag set to moa ruff log
- State changed from new to open
- Title changed from BLAST=BOOM!!@@# to Improve Moa error logging for ruff jobs
John, is this one still valid, or was it solved by changing your python version??
whatever the case is - we need to do something about how moa/ruffus shows it's errors...
cheers
M -
john.mccallum (at plantandfood) May 31st, 2011 @ 09:16 PM
Yes I think solved
-----Original Message----- From: Lighthouse [mailto:no-reply@lighthouseapp.com]
Sent: Wednesday, June 01, 2011 9:11 AM
To: John McCallum
Subject: [Moa #29] Improve Moa error logging for ruff jobs
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- 29 Improve Moa error logging for ruff jobs -----Original Message----- From: Lighthouse [mailto:no-re...