## Running Jpred Server version 4.0.0 ## --Query: d2j8ka1 --/homes/www-jpred/live4/bin/webrun -ipline 10.0.115.189 -log /homes/www-jpred/live4/public_html/results/jp_iRQHIVi/LOG -sequence /homes/www-jpred/live4/public_html/results/jp_iRQHIVi/jp_iRQHIVi.seq -format seq -id jp_iRQHIVi --TIMEOUT set at 10800 seconds --Started work on jp_iRQHIVi at Fri Apr 17 18:46:12 2015 --On machine fc-027 --format = seq >>10% complete --Running Jpred pipeline --CMD /homes/www-jpred/live4/jpred/jpred --seq jp_iRQHIVi.fasta --output jp_iRQHIVi --db uniref90 --pred-nohits --verbose path: jp_iRQHIVi.fasta output: jp_iRQHIVi db: uniref90 Time STEP0: 0 Running PSI-BLAST on query against 'uniref.filt'... Time STEP1: 1561 Time STEP2: 1561 >>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: 2392 Output the PSSM matrix from the PSI-BLAST profile... >>50% complete Time STEP4: 2392 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/4779147.1.64bit-pri.q/L9i7v3HCPq 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/4779147.1.64bit-pri.q/Dz8PflGQHR - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: #1 Number of sequences: 486 Number of columns: 175 Determining effective sequence number ... done. [470] Weighting sequences heuristically ... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [L9i7v3HCPq] Constructed a profile HMM (length 175) Average score: 145.66 bits Minimum score: -1.84 bits Maximum score: 291.69 bits Std. deviation: 59.68 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/4779147.1.64bit-pri.q/Dz8PflGQHR Output HMM file: /tmp/4779147.1.64bit-pri.q/XNwKiXIvq4 Converting to: GCG Profile .prf - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - converted L9i7v3HCPq 1 HMM(s) converted and written to /tmp/4779147.1.64bit-pri.q/XNwKiXIvq4 >>70% complete Time STEP5: 2393 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: 2393 >>80% complete --Running ncoils and multicoil 1 sequences 175 aas 21 in coil 1 sequences 175 aas 14 in coil 1 sequences 175 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_iRQHIVi.als Starting ALSCRIPT SILENT_MODE Max No. of sequences now: 500 ALscript Finished --tarring up the data >>100% complete --Finished work on jp_iRQHIVi at Fri Apr 17 19:26:20 2015 --Execution time on jp_iRQHIVi is 2408 seconds found jp_iRQHIVi.fasta Java version: 1.6.0_32 amd64 Linux 2.6.32-358.6.2.el6.x86_64 Opening file: jp_iRQHIVi.fasta 17-Apr-2015 19:33:05 jalview.util.MessageManager INFO: Getting messages for lang: en_GB java.awt.HeadlessException Added jp_iRQHIVi.concise Creating HTML image: svg.html