Hi Paul, Paul Gevers, on 2022-10-23: > @logol maintainers, those ERRORs look scary if the test passes with it. Is > that just noise, or are real problems ignored?
It looks like by default, logol expects any user to be able to
drop processing results into /var/lib/logol/results, and output
processing log in /var/log/logol. If I make them sticky world
writable, the errors go away:
drwxrwxrwt 2 root root 40 Oct 23 08:23 /var/lib/logol/results
drwxrwxrwt 2 root root 40 Oct 23 08:23 /var/log/logol
calling logol with parameters -g 1799.logol -s 1799.fasta -dna
For help, use option -h
INFO org.irisa.genouest.logol.Logol - Using configuration file:
/usr/share/logol/prolog/logol.properties
INFO org.irisa.genouest.logol.Logol - option g called with 1799.logol
INFO org.irisa.genouest.logol.Logol - option s called with 1799.fasta
INFO org.irisa.genouest.logol.Logol - No maximum solutions defined,
using defaults
INFO org.irisa.genouest.logol.Logol - option dna called
INFO org.irisa.genouest.logol.Logol - Start analyse to create grammar
analyser
Executing prolog for pre-analyse
INFO org.irisa.genouest.logol.Logol - Analyse in progress..
WARN org.irisa.genouest.logol.SequenceAnalyser - Path to suffix search
tool is not set in system environment. Will try to execute directly but may
fail if not in PATH of current user
INFO org.irisa.genouest.logol.Logol -
/tmp//1799.logol.731c3e5a-f513-4c97-af0e-1557d6881784.1-4.xml: 3
INFO org.irisa.genouest.logol.Logol - Number of output match: 3
INFO org.irisa.genouest.logol.Logol - JOB OVER !!!
INFO org.irisa.genouest.logol.Logol - RESULT FILES ARE AVAILABLE:
INFO org.irisa.genouest.logol.Logol - -
/var/lib/logol/results//1799.logol.731c3e5a-f513-4c97-af0e-1557d6881784.0-4-all.xml
calling logol with parameters -g 1799.logol -s 1799.fasta -dna
For help, use option -h
mod1()==>REP1:{_MASEQ0,#[2,2]},REP2:{?MASEQ0}:{$$[2,2]}
INFO org.irisa.genouest.logol.dispatcher.Dispatch - Sequence 1
splitted in 1 parts
INFO org.irisa.genouest.logol.dispatcher.Dispatch - Add sequence for
treatment:
/var/lib/logol/results//1799.fasta.1bd39463-6486-418a-be2e-7b5c0b49cee0
INFO org.irisa.genouest.logol.dispatcher.Dispatch - Args: -sequenceID
1
INFO org.irisa.genouest.logol.dispatcher.LocalJobManager - Run jobs
locally
INFO org.irisa.genouest.logol.dispatcher.LocalJobManager - Analyse
sequence /var/lib/logol/results//1799.fasta.1bd39463-6486-418a-be2e-7b5c0b49cee0
INFO org.irisa.genouest.logol.dispatcher.LocalJobManager - Analyse for
/var/lib/logol/results//1799.fasta.1bd39463-6486-418a-be2e-7b5c0b49cee0 is over
INFO org.irisa.genouest.logol.dispatcher.LocalJobManager - Each
sequence in bank resulted in a specific result file.
INFO org.irisa.genouest.logol.dispatcher.LocalJobManager - Result file
is available in work directory :
/var/lib/logol/results//1799.fasta.1bd39463-6486-418a-be2e-7b5c0b49cee0-XX-YY-all.xml
INFO org.irisa.genouest.logol.utils.LogolUtils - **** Results ****
INFO org.irisa.genouest.logol.utils.LogolUtils - *
/var/lib/logol/results//1799.fasta.1bd39463-6486-418a-be2e-7b5c0b49cee0.1.xml
3
INFO org.irisa.genouest.logol.utils.LogolUtils - **** Total matches:
3
INFO org.irisa.genouest.logol.dispatcher.Dispatch - Result file is
available at:
/var/lib/logol/results//1799.fasta.77dfc996-bb6b-4a83-b9a9-153d73d03e97.zip
It doesn't feel ideal, but looking through the package, these
seem intended to be adjusted to specific cluster setups. Not
sure that the default is the best, but I haven't located where
these were set in the source code in the first place.
In hope this clarifies things,
--
Étienne Mollier <[email protected]>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/7, please excuse my verbosity.
On air: Cyril - Scarlet Walking
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