## Running Jpred Server version 4.0.0 ## --Query: d1kp6a_ --/homes/www-jpred/live4/bin/webrun -ipline 10.0.115.189 -log /homes/www-jpred/live4/public_html/results/jp_m7Wh07D/LOG -sequence /homes/www-jpred/live4/public_html/results/jp_m7Wh07D/jp_m7Wh07D.seq -format seq -id jp_m7Wh07D --TIMEOUT set at 10800 seconds --Started work on jp_m7Wh07D at Fri Apr 17 19:21:52 2015 --On machine fc-042 --format = seq >>10% complete --Running Jpred pipeline --CMD /homes/www-jpred/live4/jpred/jpred --seq jp_m7Wh07D.fasta --output jp_m7Wh07D --db uniref90 --pred-nohits --verbose path: jp_m7Wh07D.fasta output: jp_m7Wh07D db: uniref90 Time STEP0: 0 Running PSI-BLAST on query against 'uniref.filt'... [blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix Time STEP1: 136 Time STEP2: 136 >>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... JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences Removing gaps in the query sequence... Outputting cleaned-up PSI_BLAST alignment... Time STEP3: 136 Output the PSSM matrix from the PSI-BLAST profile... >>50% complete Time STEP4: 136 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/4779260.1.64bit-pri.q/Cq3qktWDzJ 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/4779260.1.64bit-pri.q/EMbRYUPwcx - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: #1 Number of sequences: 2 Number of columns: 79 Determining effective sequence number ... done. [1] Weighting sequences heuristically ... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [Cq3qktWDzJ] Constructed a profile HMM (length 79) Average score: 265.45 bits Minimum score: 265.45 bits Maximum score: 265.45 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: /tmp/4779260.1.64bit-pri.q/EMbRYUPwcx Output HMM file: /tmp/4779260.1.64bit-pri.q/c9AFJiQwGn Converting to: GCG Profile .prf - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - converted Cq3qktWDzJ 1 HMM(s) converted and written to /tmp/4779260.1.64bit-pri.q/c9AFJiQwGn >>70% complete Time STEP5: 136 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: 136 >>80% complete --Running ncoils and multicoil 1 sequences 79 aas 0 in coil 1 sequences 79 aas 0 in coil 1 sequences 79 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_m7Wh07D.als Starting ALSCRIPT SILENT_MODE Max No. of sequences now: 50 ALscript Finished --tarring up the data >>100% complete --Finished work on jp_m7Wh07D at Fri Apr 17 19:24:09 2015 --Execution time on jp_m7Wh07D is 137 seconds found jp_m7Wh07D.fasta Java version: 1.6.0_32 amd64 Linux 2.6.32-358.6.2.el6.x86_64 Opening file: jp_m7Wh07D.fasta 17-Apr-2015 19:24:10 jalview.util.MessageManager INFO: Getting messages for lang: en_GB java.awt.HeadlessException Added jp_m7Wh07D.concise Creating HTML image: svg.html