## Running Jpred Server version 4.0.0 ## --Query: d1kyfa1 --/homes/www-jpred/live4/bin/webrun -ipline 10.0.115.189 -log /homes/www-jpred/live4/public_html/results/jp_nmmV_8R/LOG -sequence /homes/www-jpred/live4/public_html/results/jp_nmmV_8R/jp_nmmV_8R.seq -format seq -id jp_nmmV_8R --TIMEOUT set at 10800 seconds --Started work on jp_nmmV_8R at Fri Apr 17 20:19:53 2015 --On machine fc-038 --format = seq >>10% complete --Running Jpred pipeline --CMD /homes/www-jpred/live4/jpred/jpred --seq jp_nmmV_8R.fasta --output jp_nmmV_8R --db uniref90 --pred-nohits --verbose path: jp_nmmV_8R.fasta output: jp_nmmV_8R db: uniref90 Time STEP0: 0 Running PSI-BLAST on query against 'uniref.filt'... Time STEP1: 292 Time STEP2: 292 >>40% complete Untruncating the PSIBLAST alignments... Unmasking the alignments... Converting sequences to the same case... Remove excessive sequences... Remove sequences which too long or short... Remove redundant sequences... Removing gaps in the query sequence... Outputting cleaned-up PSI_BLAST alignment... Time STEP3: 294 Output the PSSM matrix from the PSI-BLAST profile... >>50% complete Time STEP4: 294 Running HMMer on sequences found by PSI-BLAST... 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: /tmp/4779472.1.64bit-pri.q/mk54FXMnW2 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: /tmp/4779472.1.64bit-pri.q/r4MVajVJnt - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: #1 Number of sequences: 274 Number of columns: 133 Determining effective sequence number ... done. [143] Weighting sequences heuristically ... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [mk54FXMnW2] Constructed a profile HMM (length 133) Average score: 141.23 bits Minimum score: 14.99 bits Maximum score: 235.46 bits Std. deviation: 44.46 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: /tmp/4779472.1.64bit-pri.q/r4MVajVJnt Output HMM file: /tmp/4779472.1.64bit-pri.q/UnSJ_0g0dc Converting to: GCG Profile .prf - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - converted mk54FXMnW2 1 HMM(s) converted and written to /tmp/4779472.1.64bit-pri.q/UnSJ_0g0dc >>70% complete Time STEP5: 294 Running JNet using the generated inputs from HMM and PSI-BLAST... Jnet 2.3.1 Found HMM profile data Found PSSM profile file Running final predictions! Both PSIBLAST and HMM profiles were found Accuracy will average 82.0% Jpred Finished Time STEP6: 294 >>80% complete --Running ncoils and multicoil 1 sequences 133 aas 0 in coil 1 sequences 133 aas 0 in coil 1 sequences 133 aas 0 in coil >>90% complete --creating output "JNETALIGN" data not present ALSCRIPT (ALignment to PostScript) ALSCRIPT Version 2.07d - 2nd August 2011 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@compbio.dundee.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_nmmV_8R.als Starting ALSCRIPT SILENT_MODE Max No. of sequences now: 288 ALscript Finished --tarring up the data >>100% complete --Finished work on jp_nmmV_8R at Fri Apr 17 20:24:52 2015 --Execution time on jp_nmmV_8R is 299 seconds found jp_nmmV_8R.fasta Java version: 1.6.0_32 amd64 Linux 2.6.32-358.6.2.el6.x86_64 Opening file: jp_nmmV_8R.fasta 17-Apr-2015 20:24:54 jalview.util.MessageManager INFO: Getting messages for lang: en_GB java.awt.HeadlessException Added jp_nmmV_8R.concise Creating HTML image: svg.html