1 ## Running Jpred Server version 3.0.1 ##
3 --/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
4 --TIMEOUT set at 3600 seconds
5 --Started work on jp_fSt_H_1 at Fri Apr 20 00:38:00 2012
6 --On machine fc-026.cluster.lifesci.dundee.ac.uk
9 --Running Jpred pipeline
10 --CMD /homes/www-jpred/live/jpred/jpred --seq jp_fSt_H_1.fasta --output jp_fSt_H_1 --db uniref90 --pred-nohits --verbose
11 path: jp_fSt_H_1.fasta
14 Running PSI-BLAST on query against 'uniref90.filt'...
15 [blastpgp] WARNING: posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
17 blastpgp error.log file was not empty
19 JPRED: no PSI-BLAST hits found. Continuing with single query sequence only.
22 Running HMMer on query...
23 hmmbuild - build a hidden Markov model from an alignment
24 HMMER 2.3.2 (Oct 2003)
25 Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
26 Freely distributed under the GNU General Public License (GPL)
27 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
28 Alignment file: jp_fSt_H_1.fasta
30 Search algorithm configuration: Multiple domain (hmmls)
31 Model construction strategy: Fast/ad hoc (gapmax 1.00)
32 Null model used: (default)
34 Sequence weighting method: BLOSUM filter at 0.62 id
35 New HMM file: /local/tmp/1663474.1.64bit-pri.q/Rfyw3iB1aW
36 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
39 Number of sequences: 1
42 Determining effective sequence number ... done. [1]
43 Weighting sequences heuristically ... done.
44 Constructing model architecture ... done.
45 Converting counts to probabilities ... done.
46 Setting model name, etc. ... done. [jp_fSt_H_1]
48 Constructed a profile HMM (length 20)
49 Average score: 56.91 bits
50 Minimum score: 56.91 bits
51 Maximum score: 56.91 bits
52 Std. deviation: 0.00 bits
54 Finalizing model configuration ... done.
55 Saving model to file ... done.
58 hmmconvert - convert between profile HMM file formats
59 HMMER 2.3.2 (Oct 2003)
60 Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
61 Freely distributed under the GNU General Public License (GPL)
62 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
63 Input HMM file: /local/tmp/1663474.1.64bit-pri.q/Rfyw3iB1aW
64 Output HMM file: /local/tmp/1663474.1.64bit-pri.q/DFOxHLRNxl
65 Converting to: GCG Profile .prf
66 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
68 - converted jp_fSt_H_1
70 1 HMM(s) converted and written to /local/tmp/1663474.1.64bit-pri.q/DFOxHLRNxl
72 Running JNet using the generated inputs from HMM only...
74 Found HMM profile data
75 Running final predictions!
78 WARNING!: Only using the HMM profile
79 Accuracy will average 79.6%
83 --Running ncoils and multicoil
84 1 sequences 20 aas 0 in coil
85 1 sequences 20 aas 0 in coil
86 1 sequences 20 aas 0 in coil
89 "JNETALIGN" data not present
90 "JNETPSSM" data not present
92 ALSCRIPT (ALignment to PostScript)
93 ALSCRIPT Version 2.07a - 21 March 2000
95 See ALSCRIPT.DOC for details
97 Please Reference: Barton, G. J. (1993), Protein Engineering, 6, 37-40.
101 Copyright: Geoffrey J. Barton (1992,1997)
102 email: geoff@ebi.ac.uk
105 Maximum number of sequences: 500 (Change using MAX_NSEQ command)
106 Maximum sequence length: 8000 (Change using MAX_SEQ_LEN command)
107 Maximum identifier length: 50 (Change using MAX_ID_LEN command)
108 ALscript Command File: jp_fSt_H_1.als
111 Max No. of sequences now: 50
113 --tarring up the data