## Running Jpred Server version 4.0.0 ##

--/homes/www-jpred/live4_migration/bin/webrun -ipline 131.212.251.71 -log /homes/www-jpred/live4_migration/public_html/results/jp_6VX6dfa/LOG -sequence /homes/www-jpred/live4_migration/public_html/results/jp_6VX6dfa/jp_6VX6dfa.seq -format seq -id jp_6VX6dfa --cache-no-remote
--TIMEOUT set at 10800 seconds
--Started work on jp_6VX6dfa at Tue Jun  2 18:15:45 2026
--On machine gpu-43.compute.dundee.ac.uk
--format = seq
>>10% complete
SequenceBased_CheckingCache
--Running Jpred pipeline
--CMD /homes/www-jpred/live4_migration/jpred/jpred --seq jp_6VX6dfa.fasta --output jp_6VX6dfa --db uniref90 --pred-nohits --verbose
DB is global.
Host: gpu-43
path: jp_6VX6dfa.fasta
output: jp_6VX6dfa
db: uniref90
Changed DB to local.
Time STEP0: 0
Running PSI-BLAST on query against 'uniref.filt'...
Time STEP1: 158
Time STEP2: 158
>>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: 190
Output the PSSM matrix from the PSI-BLAST profile...
>>50% complete
Time STEP4: 190
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)
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Alignment file:                    /tmp/3778430.1.rhel9.q/fzzPrAztZu
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/3778430.1.rhel9.q/w4F4YYk9AH 
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Alignment:           #1
Number of sequences: 863
Number of columns:   116

Determining effective sequence number    ... done. [269]
Weighting sequences heuristically        ... done.
Constructing model architecture          ... done.
Converting counts to probabilities       ... done.
Setting model name, etc.                 ... done. [fzzPrAztZu]

Constructed a profile HMM (length 116)
Average score:      101.35 bits
Minimum score:       23.97 bits
Maximum score:      181.65 bits
Std. deviation:      24.17 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)
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Input HMM file:           /tmp/3778430.1.rhel9.q/w4F4YYk9AH
Output HMM file:          /tmp/3778430.1.rhel9.q/TVgJY_6zrq
Converting to:            GCG Profile .prf
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 - converted fzzPrAztZu

1 HMM(s) converted and written to /tmp/3778430.1.rhel9.q/TVgJY_6zrq
>>70% complete
Time STEP5: 191
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: 191
>>80% complete
--Running ncoils and multicoil
       1 sequences      116 aas        0 in coil
       1 sequences      116 aas        0 in coil
       1 sequences      116 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_6VX6dfa.als
Starting ALSCRIPT
SILENT_MODE
Max No. of sequences now:	877
ALscript Finished
--tarring up the data
>>100% complete
--Finished work on jp_6VX6dfa at Tue Jun  2 18:18:58 2026
--Execution time on jp_6VX6dfa is 193 seconds
found jp_6VX6dfa.fasta
Java version: 17.0.15
amd64 Linux 5.14.0-427.37.1.el9_4.x86_64
Opening file: jp_6VX6dfa.fasta
Jun 02, 2026 6:18:59 PM jalview.util.MessageManager <clinit>
INFO: Getting messages for lang: en_US
java.awt.HeadlessException
Added jp_6VX6dfa.concise
Creating HTML image: svg.html
