From: PARSONS_A@snd01.pcr.co.uk
Newsgroups: bionet.software
Subject: GCG synchronisation problem
Date: 5 Jan 93 09:33:09 GMT
Distribution: bionet
Original-To: BIO-SOFT <BIO-SOFT@UK.AC.DARESBURY>

Happy New Year Neteers,

I have had no joy out of GCG on this one - anyone had anyexperience of this 
particular error whilst using GCG and (a) what it might mean and (b) how it
affects the quality of the results that I get?

Thanks in Advance,

Tony Parsons <<parsons_a@snd01.pcr.co.uk = Pfizer Central Research UK>>

Details.....

I was trying to search PIR using FASTA and got the following error :-

 *** ERROR in SQNext. Sequence reading is out of synchronization. 


Any ideas what is going on?

Log file follows...

Tony Parsons - Pfizer central Research  (parsons_a@snd01.pcr.co.uk)

-------------------------  log of session  -----------------------------------

 		                WELCOME TO GCG
                      Sequence Analysis Software Package 
                           Version 7.1,  March, 1992

         (c)1982, 1983, 1984, 1985, 1986, 1987, 1989, 1991, 1992
              Genetics Computer Group, Inc.  All rights reserved.

         Published research assisted by this software should cite:
  Devereux, Haeberli and Smithies (1984). A Comprehensive Set of Sequence 
    Analysis Programs for the VAX. Nucleic Acids Research 12(1); 387-395 

Databases available: 
GenBank            Release 73.0 (9/92)  PIR-Protein        Release 34.0 (10/92)
EMBL (Modified)    Release 32.0 (9/92)  SwissProt          Release 23.0 ( 8/92)
PIR-Nucleic        Release 36.0 (3/90)  Vecbase            Release  3.0 ( 8/87)
PROSITE            Release  9.2 (9/92)  REBASE restriction enzymes 9210 (10/92)
			MIPSX  34.0  (9/92)
             Help is available with the command $ GenHelp

PROBLEMS WITH NEW SOFTWARE or DATABASES        email: PARSONS_A   tel - 6871
 Running Fasta  using : 
...
/INfile=ul08.gcg
/BEGin=1
/END=750
/INfile2=p:*
/WORd=2
/LIStsize=40
/OUTfile=Ul08.Fasta
/Default


 *** ERROR in SQNext. Sequence reading is out of synchronization. 

 



(Peptide) FASTA of: Ul08.Gcg  from: 1   to: 750  December 8, 1992  15:09
 TO: p:*  Sequences:        223  Symbols:     30,658  Word Size: 2


Score Init1 Initn
<  2     0     0:
   4     0     0:
   6     0     0:
   8     0     0:
  10     0     0:
  12     0     0:
  14     0     0:
  16     1     1:=
  18     4     4:==
  20    12    12:======
  22    26    26:=============
  24    21    21:===========
  26    35    35:==================
  28    30    30:===============
  30    10    10:=====
  32    44    43:======================
  34     7     6:===-
  36     4     2:=-
  38    10     6:===--
  40     7     3:==--
  42     4     5:==+
  44     2     2:=
  46     1     1:=
  48     5     6:===
  50     0     2:+
  52     0     1:+
  54     0     1:+
  56     0     1:+
  58     0     0:
  60     0     1:+
  62     0     1:+
  64     0     0:
  66     0     1:+
  68     0     1:+
  70     0     0:
  72     0     1:+
  74     0     0:
  76     0     0:
  78     0     0:
  80     0     0:
> 80     0     0:
 mean initn score:  23.8 (2.83)
 mean init1 score:  23.8 (2.83)


The best scores are:				            init1 initn opt

Pir1:Cbms  Cytochrome b - Mouse mitochondrion (SGC1)          39    72    40
Pir1:Cbrt  Cytochrome b - Rat mitochondrion (SGC1)            39    68    40
Pir1:Cbqfr  Cytochrome b - Rhodospirillum rubrum              39    66    41
Pir1:Cbhu  Cytochrome b - Human mitochondrion (SGC1)          37    62    39
Pir1:Wmrz17  Cytochrome b6-f complex 17K protein - Rice c...  44    59    66
Pir1:O4hud1  Debrisoquine 4-hydroxylase (EC 1.14.14.-) cy...  37    55    37
Pir1:Cbbo  Cytochrome b - Bovine mitochondrion (SGC1)         39    54    40
Pir1:Wmlv17  Cytochrome b6-f complex 17K protein - Liverw...  37    52    57
Pir1:Cbxl  Cytochrome b - African clawed frog mitochondri...  38    49    42
Pir1:Ccqfct  Cytochrome c' - Rhodocyclus tenuis               35    49    35
Pir1:Cbboc6  Cytochrome b-c1 complex, 6.4K protein - Bovine   36    48    41
Pir1:Cblv55  Cytochrome b559 component E - Liverwort (Mar...  47    47    50
Pir1:Cbobe  Cytochrome b - Evening primrose mitochondrion     47    47    61
Pir1:Cbnt55  Cytochrome b559 component E - Common tobacco...  47    47    50
Pir1:Cbrz55  Cytochrome b559 component E - Rice chloroplast   47    47    50
Pir1:Cbvf  Cytochrome b - Fava bean mitochondrion             47    47    61
Pir1:Wmnt17  Cytochrome b6-f complex 17K protein - Common...  45    45    67
Pir1:Ccrfpp  Cytochrome c' - Rhodobacter capsulatus           33    43    33
Pir1:Cclm  Cytochrome c - Pacific lamprey                     43    43    46
Pir1:Cbutb  Cytochrome b - Trypanosoma brucei mitochondri...  32    42    42
Pir1:Rdbyun  Ubiquinol--cytochrome-c reductase (EC 1.10.2...  42    42    42
Pir1:Wmsp17  Cytochrome b6-f complex 17K protein - Spinac...  41    41    67
Pir1:Cbyb55  Cytochrome b559 component psbE - Synechocyst...  41    41    48
Pir1:O4psz  Denitrification system component nirT - Pseud...  41    41    51
Pir1:Ccps5a  Cytochrome c551 - Pseudomonas aeruginosa         40    40    41
Pir1:Cbrz  Cytochrome b - Rice mitochondrion                  39    39    41
Pir1:Cbzm  Cytochrome b - Maize mitochondrion                 39    39    41
Pir1:Ccps5f  Cytochrome c551 - Pseudomonas fluorescens bi...  38    38    49
Pir1:Cbbo5  Cytochrome b5 - Bovine                            38    38    52
Pir1:Ccps5d  Cytochrome c551 - Pseudomonas sp.                38    38    49
Pir1:Ccbf6  Cytochrome c6 - Yellow-green alga (Bumillerio...  37    37    39
Pir1:Ccps5s  Cytochrome c551 - Pseudomonas stutzeri (stra...  37    37    52
Pir1:Ccps5b  Cytochrome c551 precursor - Pseudomonas stut...  37    37    47
Pir1:Wmkl17  Cytochrome b6-f complex 17K protein - Chlore...  36    36    38
Pir1:Cctw5t  Cytochrome c552 - Thermus aquaticus              36    36    36
Pir1:Cblv6  Cytochrome b6 - Liverwort (Marchantia polymor...  34    34    36
Pir1:Ccck  Cytochrome c - Yeast (Issatchenkia orientalis)     33    33    36
Pir1:Ccus  Cytochrome c - Smut fungus (Ustilago sphaerogena)  33    33    34
Pir1:Cceg  Cytochrome c - Euglena gracilis                    33    33    41
Pir1:Cchq  Cytochrome c - Yeast (Hansenula anomala)           33    33    37

Aligning...
 CPU time:  0:00:19
 Output File: Ul08.Fasta
  PARSONS_A    job terminated at  8-DEC-1992 15:13:16.77

  Accounting information:
  Buffered I/O count:             457         Peak working set size:   12603
  Direct I/O count:              1919         Peak page file size:     21702
  Page faults:                  15293         Mounted volumes:             0
  Charged CPU time:           0 00:00:29.73   Elapsed time:     0 00:05:30.12
Newsgroups: bionet.software