X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=examples%2Funres%2FCSA%2FGAB%2FCSA%2Fglobal%2Frestrained%2Fjpred_prediction%2FLOG;fp=examples%2Funres%2FCSA%2FGAB%2FCSA%2Fglobal%2Frestrained%2Fjpred_prediction%2FLOG;h=0000000000000000000000000000000000000000;hb=c5370e6422f68c03f5801e5e8b127a5ba478695b;hp=bba1b436fde7541c19c326183911fec5d2dca97f;hpb=866c6bb3445c32af6d43b6eea1c565ae7d78e7f2;p=unres.git

diff --git a/examples/unres/CSA/GAB/CSA/global/restrained/jpred_prediction/LOG b/examples/unres/CSA/GAB/CSA/global/restrained/jpred_prediction/LOG
deleted file mode 100644
index bba1b43..0000000
--- a/examples/unres/CSA/GAB/CSA/global/restrained/jpred_prediction/LOG
+++ /dev/null
@@ -1,113 +0,0 @@
-## Running Jpred Server version 3.0.1 ##
-
---/homes/www-jpred/live/bin/webrun --email --log /homes/www-jpred/live/public_html/results/jp_fSt_H_1/LOG --sequence /homes/www-jpred/live/public_html/results/jp_fSt_H_1/jp_fSt_H_1.seq --format seq --id jp_fSt_H_1
---TIMEOUT set at 3600 seconds
---Started work on jp_fSt_H_1 at Fri Apr 20 00:38:00 2012
---On machine fc-026.cluster.lifesci.dundee.ac.uk
---format = seq
->>10% complete
---Running Jpred pipeline
---CMD /homes/www-jpred/live/jpred/jpred --seq jp_fSt_H_1.fasta --output jp_fSt_H_1 --db uniref90 --pred-nohits --verbose
-path: jp_fSt_H_1.fasta
-output: jp_fSt_H_1
-db: uniref90
-Running PSI-BLAST on query against 'uniref90.filt'...
-[blastpgp] WARNING: posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
-
-blastpgp error.log file was not empty
-
-JPRED: no PSI-BLAST hits found. Continuing with single query sequence only.
-
->>50% complete
-Running HMMer on query...
-hmmbuild - build a hidden Markov model from an alignment
-HMMER 2.3.2 (Oct 2003)
-Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
-Freely distributed under the GNU General Public License (GPL)
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Alignment file:                    jp_fSt_H_1.fasta
-File format:                       a2m
-Search algorithm configuration:    Multiple domain (hmmls)
-Model construction strategy:       Fast/ad hoc (gapmax 1.00)
-Null model used:                   (default)
-Prior used:                        (default)
-Sequence weighting method:         BLOSUM filter at 0.62 id
-New HMM file:                      /local/tmp/1663474.1.64bit-pri.q/Rfyw3iB1aW 
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
-Alignment:           #1
-Number of sequences: 1
-Number of columns:   20
-
-Determining effective sequence number    ... done. [1]
-Weighting sequences heuristically        ... done.
-Constructing model architecture          ... done.
-Converting counts to probabilities       ... done.
-Setting model name, etc.                 ... done. [jp_fSt_H_1]
-
-Constructed a profile HMM (length 20)
-Average score:       56.91 bits
-Minimum score:       56.91 bits
-Maximum score:       56.91 bits
-Std. deviation:       0.00 bits
-
-Finalizing model configuration           ... done.
-Saving model to file                     ... done.
-//
-
-hmmconvert - convert between profile HMM file formats
-HMMER 2.3.2 (Oct 2003)
-Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
-Freely distributed under the GNU General Public License (GPL)
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Input HMM file:           /local/tmp/1663474.1.64bit-pri.q/Rfyw3iB1aW
-Output HMM file:          /local/tmp/1663474.1.64bit-pri.q/DFOxHLRNxl
-Converting to:            GCG Profile .prf
-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
- - converted jp_fSt_H_1
-
-1 HMM(s) converted and written to /local/tmp/1663474.1.64bit-pri.q/DFOxHLRNxl
->>70% complete
-Running JNet using the generated inputs from HMM only...
-Jnet 2.2
-Found HMM profile data
-Running final predictions!
-
-
-WARNING!: Only using the HMM profile
-Accuracy will average 79.6%
-
-Jpred Finished
->>80% complete
---Running ncoils and multicoil
-       1 sequences       20 aas        0 in coil
-       1 sequences       20 aas        0 in coil
-       1 sequences       20 aas        0 in coil
->>90% complete
---creating output
-"JNETALIGN" data not present
-"JNETPSSM" data not present
-
-ALSCRIPT  (ALignment to PostScript)
-ALSCRIPT Version 2.07a - 21 March 2000
-
-See ALSCRIPT.DOC for details
-
-Please Reference: Barton, G. J. (1993), Protein Engineering, 6, 37-40.
-
-By: G. J. Barton
-
-Copyright: Geoffrey J. Barton (1992,1997)
-email: geoff@ebi.ac.uk
-
-Initial Defaults:
-Maximum number of sequences:	 500 	(Change using MAX_NSEQ command)
-Maximum sequence length:	 8000 	(Change using MAX_SEQ_LEN command)
-Maximum identifier length:	 50 	(Change using MAX_ID_LEN command)
-ALscript Command File: jp_fSt_H_1.als
-Starting ALSCRIPT
-SILENT_MODE
-Max No. of sequences now:	50
-ALscript Finished
---tarring up the data