Merge branch 'prerelease-3.2.1' into czarek

[unres.git] / examples / unres / CSA / GAB / global / restrained / jpred_prediction / LOG

diff --git a/examples/unres/CSA/GAB/global/restrained/jpred_prediction/LOG b/examples/unres/CSA/GAB/global/restrained/jpred_prediction/LOG
new file mode 100644 (file)
index 0000000..bba1b43
--- /dev/null
+++ b/examples/unres/CSA/GAB/global/restrained/jpred_prediction/LOG
@@ -0,0 +1,113 @@
+## 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