## Running Jpred Server version 4.0.0 ## --Query: d1gqia2 --/homes/www-jpred/live4/bin/webrun -ipline 10.0.115.189 -log /homes/www-jpred/live4/public_html/results/jp_u_nyAWX/LOG -sequence /homes/www-jpred/live4/public_html/results/jp_u_nyAWX/jp_u_nyAWX.seq -format seq -id jp_u_nyAWX --TIMEOUT set at 10800 seconds --Started work on jp_u_nyAWX at Fri Apr 17 18:16:22 2015 --On machine fc-019 --format = seq >>10% complete --Running Jpred pipeline --CMD /homes/www-jpred/live4/jpred/jpred --seq jp_u_nyAWX.fasta --output jp_u_nyAWX --db uniref90 --pred-nohits --verbose path: jp_u_nyAWX.fasta output: jp_u_nyAWX db: uniref90 Time STEP0: 0 Running PSI-BLAST on query against 'uniref.filt'... Time STEP1: 362 Time STEP2: 362 >>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: 392 Output the PSSM matrix from the PSI-BLAST profile... >>50% complete Time STEP4: 392 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/4778924.1.64bit-pri.q/l2XVjZebj6 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/4778924.1.64bit-pri.q/RlMr4_dWah - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: #1 Number of sequences: 1104 Number of columns: 147 Determining effective sequence number ... done. [808] Weighting sequences heuristically ... [big alignment! doing PB]... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [l2XVjZebj6] Constructed a profile HMM (length 147) Average score: 96.51 bits Minimum score: 4.09 bits Maximum score: 225.63 bits Std. deviation: 39.91 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/4778924.1.64bit-pri.q/RlMr4_dWah Output HMM file: /tmp/4778924.1.64bit-pri.q/Km0eF05R7A Converting to: GCG Profile .prf - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - converted l2XVjZebj6 1 HMM(s) converted and written to /tmp/4778924.1.64bit-pri.q/Km0eF05R7A >>70% complete Time STEP5: 393 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: 393 >>80% complete --Running ncoils and multicoil 1 sequences 147 aas 0 in coil 1 sequences 147 aas 0 in coil 1 sequences 147 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_u_nyAWX.als Starting ALSCRIPT SILENT_MODE Max No. of sequences now: 1118 ALscript Finished --tarring up the data >>100% complete --Finished work on jp_u_nyAWX at Fri Apr 17 18:23:14 2015 --Execution time on jp_u_nyAWX is 412 seconds found jp_u_nyAWX.fasta Java version: 1.6.0_32 amd64 Linux 2.6.32-358.6.2.el6.x86_64 Opening file: jp_u_nyAWX.fasta 17-Apr-2015 18:23:17 jalview.util.MessageManager INFO: Getting messages for lang: en_GB java.awt.HeadlessException Added jp_u_nyAWX.concise Creating HTML image: svg.html