## Running Jpred Server version 4.0.0 ## --Query: d1pm4a_ --/homes/www-jpred/live4/bin/webrun -ipline 10.0.115.189 -log /homes/www-jpred/live4/public_html/results/jp_QzxzLfC/LOG -sequence /homes/www-jpred/live4/public_html/results/jp_QzxzLfC/jp_QzxzLfC.seq -format seq -id jp_QzxzLfC --TIMEOUT set at 10800 seconds --Started work on jp_QzxzLfC at Fri Apr 17 18:25:52 2015 --On machine fc-003 --format = seq >>10% complete --Running Jpred pipeline --CMD /homes/www-jpred/live4/jpred/jpred --seq jp_QzxzLfC.fasta --output jp_QzxzLfC --db uniref90 --pred-nohits --verbose path: jp_QzxzLfC.fasta output: jp_QzxzLfC db: uniref90 Time STEP0: 0 Running PSI-BLAST on query against 'uniref.filt'... Time STEP1: 89 Time STEP2: 89 >>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: 89 Output the PSSM matrix from the PSI-BLAST profile... >>50% complete Time STEP4: 89 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/4778955.1.64bit-pri.q/oTy90EFw7U 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/4778955.1.64bit-pri.q/Mpcdn5iZs3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment: #1 Number of sequences: 3 Number of columns: 117 Determining effective sequence number ... done. [1] Weighting sequences heuristically ... done. Constructing model architecture ... done. Converting counts to probabilities ... done. Setting model name, etc. ... done. [oTy90EFw7U] Constructed a profile HMM (length 117) Average score: 343.13 bits Minimum score: 324.48 bits Maximum score: 352.45 bits Std. deviation: 16.14 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/4778955.1.64bit-pri.q/Mpcdn5iZs3 Output HMM file: /tmp/4778955.1.64bit-pri.q/DjJFmC0pEs Converting to: GCG Profile .prf - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - converted oTy90EFw7U 1 HMM(s) converted and written to /tmp/4778955.1.64bit-pri.q/DjJFmC0pEs >>70% complete Time STEP5: 89 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: 89 >>80% complete --Running ncoils and multicoil 1 sequences 117 aas 0 in coil 1 sequences 117 aas 0 in coil 1 sequences 117 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_QzxzLfC.als Starting ALSCRIPT SILENT_MODE Max No. of sequences now: 50 ALscript Finished --tarring up the data >>100% complete --Finished work on jp_QzxzLfC at Fri Apr 17 18:27:22 2015 --Execution time on jp_QzxzLfC is 90 seconds found jp_QzxzLfC.fasta Java version: 1.6.0_32 amd64 Linux 2.6.32-358.6.2.el6.x86_64 Opening file: jp_QzxzLfC.fasta 17-Apr-2015 18:27:23 jalview.util.MessageManager INFO: Getting messages for lang: en_GB java.awt.HeadlessException Added jp_QzxzLfC.concise Creating HTML image: svg.html