## Running Jpred Server version 4.0.0 ## --Query: d1m1fa_ --/homes/www-jpred/live4/bin/webrun -ipline 10.0.115.189 -log /homes/www-jpred/live4/public_html/results/jp_SHa3wDM/LOG -sequence /homes/www-jpred/live4/public_html/results/jp_SHa3wDM/jp_SHa3wDM.seq -format seq -id jp_SHa3wDM --TIMEOUT set at 10800 seconds --Started work on jp_SHa3wDM at Fri Apr 17 17:22:12 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_SHa3wDM.fasta --output jp_SHa3wDM --db uniref90 --pred-nohits --verbose path: jp_SHa3wDM.fasta output: jp_SHa3wDM db: uniref90 Time STEP0: 0 Running PSI-BLAST on query against 'uniref.filt'... Time STEP1: 1454 Time STEP2: 1454 >>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: 1502 Output the PSSM matrix from the PSI-BLAST profile... >>50% complete Time STEP4: 1502 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/4778720.1.c6145.q/yYxy1Cl2Vp 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/4778720.1.c6145.q/4JJJpzYHLh - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: #1 Number of sequences: 992 Number of columns: 107 Determining effective sequence number ... done. [517] Weighting sequences heuristically ... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [yYxy1Cl2Vp] Constructed a profile HMM (length 107) Average score: 115.07 bits Minimum score: 9.61 bits Maximum score: 194.16 bits Std. deviation: 33.30 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/4778720.1.c6145.q/4JJJpzYHLh Output HMM file: /tmp/4778720.1.c6145.q/t9xYUXsrWM Converting to: GCG Profile .prf - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - converted yYxy1Cl2Vp 1 HMM(s) converted and written to /tmp/4778720.1.c6145.q/t9xYUXsrWM >>70% complete Time STEP5: 1503 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: 1503 >>80% complete --Running ncoils and multicoil 1 sequences 107 aas 0 in coil 1 sequences 107 aas 0 in coil 1 sequences 107 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_SHa3wDM.als Starting ALSCRIPT SILENT_MODE Max No. of sequences now: 1006 ALscript Finished --tarring up the data >>100% complete --Finished work on jp_SHa3wDM at Fri Apr 17 17:47:34 2015 --Execution time on jp_SHa3wDM is 1522 seconds found jp_SHa3wDM.fasta Java version: 1.6.0_32 amd64 Linux 2.6.32-358.6.2.el6.x86_64 Opening file: jp_SHa3wDM.fasta 17-Apr-2015 17:47:40 jalview.util.MessageManager INFO: Getting messages for lang: en_GB java.awt.HeadlessException Added jp_SHa3wDM.concise Creating HTML image: svg.html