## 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