## Running Jpred Server version 4.0.0 ## --Query: d1ocya_ --/homes/www-jpred/live4/bin/webrun -ipline 10.0.115.189 -log /homes/www-jpred/live4/public_html/results/jp_GYvgZlt/LOG -sequence /homes/www-jpred/live4/public_html/results/jp_GYvgZlt/jp_GYvgZlt.seq -format seq -id jp_GYvgZlt --TIMEOUT set at 10800 seconds --Started work on jp_GYvgZlt at Fri Apr 17 16:34:14 2015 --On machine pe-004.cluster.lifesci.dundee.ac.uk. --format = seq >>10% complete --Running Jpred pipeline --CMD /homes/www-jpred/live4/jpred/jpred --seq jp_GYvgZlt.fasta --output jp_GYvgZlt --db uniref90 --pred-nohits --verbose path: jp_GYvgZlt.fasta output: jp_GYvgZlt db: uniref90 Time STEP0: 0 Running PSI-BLAST on query against 'uniref.filt'... Time STEP1: 2808 Time STEP2: 2808 >>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: 2885 Output the PSSM matrix from the PSI-BLAST profile... >>50% complete Time STEP4: 2885 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/4778519.1.c6145.q/40hc84T7z4 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/4778519.1.c6145.q/5kWVluPT6H - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: #1 Number of sequences: 1092 Number of columns: 198 Determining effective sequence number ... done. [634] Weighting sequences heuristically ... [big alignment! doing PB]... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [40hc84T7z4] Constructed a profile HMM (length 198) Average score: 146.55 bits Minimum score: 16.77 bits Maximum score: 255.91 bits Std. deviation: 43.96 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/4778519.1.c6145.q/5kWVluPT6H Output HMM file: /tmp/4778519.1.c6145.q/gVQwwrzhPx Converting to: GCG Profile .prf - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - converted 40hc84T7z4 1 HMM(s) converted and written to /tmp/4778519.1.c6145.q/gVQwwrzhPx >>70% complete Time STEP5: 2886 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: 2887 >>80% complete --Running ncoils and multicoil 1 sequences 198 aas 0 in coil 1 sequences 198 aas 0 in coil 1 sequences 198 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_GYvgZlt.als Starting ALSCRIPT SILENT_MODE Max No. of sequences now: 1106 ALscript Finished --tarring up the data >>100% complete --Finished work on jp_GYvgZlt at Fri Apr 17 17:22:54 2015 --Execution time on jp_GYvgZlt is 2920 seconds found jp_GYvgZlt.fasta Java version: 1.6.0_32 amd64 Linux 2.6.32-358.6.2.el6.x86_64 Opening file: jp_GYvgZlt.fasta 17-Apr-2015 17:23:12 jalview.util.MessageManager INFO: Getting messages for lang: en_GB java.awt.HeadlessException Added jp_GYvgZlt.concise Creating HTML image: svg.html