From: ftp-bimas.cit.nih.gov                        Last mod: November 28, 1995

                LINKAGE/FASTLINK Troubleshooting
                Alejandro A. Schaffer

LINKAGE and FASTLINK produce lots of different error messages that may
be difficult to understand. This file briefly summarizes the error
messages in five groups.

1. Error messages in LINKAGE that were inherited in FASTLINK
These all have numbers, although the numbers are not printed out.

2. Error messages new to FASTLINK

3. Incompatibility errors in UNKNOWN

4. Error messages in lsp. These error messages are especially cryptic.
They all have a 6 letter error code and little other information.

5. Error messages in lrp. Unfortunately, the error printing routine
   ignores a lot of useful diagnostic information that is passed to it.

The way to use this file is to note down the error message you
got and then use grep to find it in this file to figure out what may be wrong.

Almost all the common errors in the first and third categories are
white-space placement errors. Thus the error message should be interpreted
only as a clue of what is the vicinity of the error in the
data files.

    |*|  Error Messages in LINKAGE Main Programs and UNKNOWN

The main programs and UNKNOWN use the same error routine, although in
practice some of the errors can occur only one place or the other.
This section describes the errors that have been reported in LINKAGE
all along. Other errors may be found in the next two sections


Error Number:0 
Message: Number of loci 17 exceeds the constant maxlocus
What it means: maxlocus is the maximum number of loci that can be used
               simultaneously in a run. You can increase maxlocus
               by changing commondefs.h or Makefile.


Error Number:1
Message: Number of loci read . Less than minimum of 1
What it means: The first number in locus file (datain.dat) or datafile.dat 
               is mangled; you probably erred in using preplink to
               prepare the locus file.


Error Number:2
Message: Error detected reading loci order. Locus number 17
         in position 5 exceeds number of loci
What it means: The third line of your locus file has no locus 17 on it, but you
               asked lcp to use hat locus. This probably occurred
               by using a text editor to add new loci to the locus file
               and forgetting to update the locus order on line 3.

Error Number:3
Message: Error detected reading loci order. Illegal locus number 17
         in position 2
What it mens: Your lcp script wants to use locus 17, but your locus
              file does not have 17 loci described. This can occur when
              you mix-up data sets.

Error Number:4
Message: Error detected reading loci order. Locus number repeated in
         positions 2 and 3
What it means: Your probably made a typo in lcp and used the same locus in two
               different positions of the fixed locus map

Error Number:5
Message: Error detected reading locus description. Illegal locus type 7 for
         locus 6
What it means: The first number in the description of each locus in the 
               locus file must be 1,2,3,or 4.

Error Number:6
Message: Error detected reading locus description for system 7. Number 
         of alleles  25 exceeds maxall
What it means: One of your loci is described as having 25 alleles in the
               locus file. maxall is a constant limiting the maximum
               number of alleles at a locus. You can increase maxall to
               more than 25, by changing unknown.c, commondefs.h, or
               Makefile. 
Important: Versions of FASTLINK  earlier than 3.0P cannot handle maxall > 31.

Error Number:7
Message: Error detected reading locus description for system 6. 
         Illegal number of alleles  0
What it means: One of your loci is described as having 0 alleles.
               This is likely a white space error in the locus file
               causing the wrong string to be interpreted as the number 
               of alleles

Error Number:8
Message: Error detected reading locus description for system 6. 
         Number of factors  17 exceeds maxfact
What it means: Similar to error number 6. There is a constant maxfact
         that is the maximum number of binary factors allowed at a
         locus of that type. You can change maxfact in unknown.c
         commondefs.h and Makefile.
Important: Set maxfact and maxall to the same value; FASTLINK cannot
           handle maxfact > 31.

Error Number:9
Message: Error detected reading locus description for system 6.
         Illegal number of factors  0
What it means: Very similar to error number 7. 7 appears for numbered allele
               loci, while 9 appears for binary factors loci.

Error Number:10
Message: Error detected reading locus description for system 6.
         Alleles not codominant.
THIS ERROR IS OBSOLETE

Error Number:11
Message: Error detected reading pedigree record 17. Illegal code for sex 8.
What it means: The column for gender is the eighth column in pedin.dat
  and the fifth column in the input to MAKEPED. Error 11 can be caused by 
  entering either the wrong value for the gender or having a
  white-space error that causes the wrong column to be read as gender.
  Be especially careful to have exactly one carriage return after the
  entry for each person, and no other carriage returns.

Error Number:12
Message:  Error detected reading pedigree record at pedigree 17.
          Maximum number of pedigree records exceeded
What it means: The maximum number of pedigrees is determined by
         the constant maxind, which can be changed in commondefs.h
         unknown.c, and Makefile. You may have truly exceeded maxped or
         you may have a white-space error.


Error Number:13
Message: Error detected reading pedigree record 501. 
         Maximum number of individuals exceeded,
What it means: Similar to error 12. The maximum number of people in a
         a data set is determined by the constant maxped. 

Error Number:14
Message: Error detected reading pedigree record 300. Illegal binary factor
         code 2.
What it means: Binary factors must be 0 or 1. Usually this error occurs
        because of a white-space problem that causes lsp to look in the
        wrong columns.

Error Number:15
Message: Error detected reading pedigree record 300. 
         No allelic pair for genotype.
THIS ERROR IS OBSOLETE

Error Number:16
Message: Error detected reading pedigree record 300.
          Allele number 25 exceeds maxall.
What it means: A numbered allele cannot have a value larger than the
               constant maxall. See error 6.

Error Number:17
Message: Error detected reading pedigree record 300.
         Illegal allele number -1.
What it means: You have a negative allele number in your input file.
               I have not figured out any plausible circumstances under which
               this error could occur.

Error Number: 18
Message: Number of systems after factorization 60 exceeds maxsystem
THIS ERROR IS OBSOLETE

Error Number:19
Message: Number of systems after factorization 0 less than minimum of 1.
THIS ERROR IS OBSOLETE

Error Number:20
Message: Number of recombination types 100 exceeds maxrectype
THIS ERROR IS OBSOLETE

Error Number:21
Message: Number of recombination types 0 less than minimum of 1.
THIS ERROR IS OBSOLETE

Error Number: 22
Message: End of file detected in tempdat by procedure 
         readthg before all data found
THIS ERROR IS OBSOLETE

Error Number: 23
Message: Error detected reading iterated locus in datafile.
         Value (7) greater than nlocus
What it means: You are using ILINK to estimate allele
         frequencies or something else, and you gave a locus number
         that is too high.

Error Number: 24
Message: Error detected reading iterated locus in datafile. 
         Illegal value (-1)\n",
What it means: Similar to error 23, but this one occurs when
         the locus number is negative.
         I have not figured out any plausible circumstances under which
         this error could occur.

Error Number: 25
Message: Number of iterated parameters greater then maxn.
What it means: The number of parameters that you can simultaneously
        estimate in ILINK is determined by the constant maxn, which can
        be increased in ildefs.h or Makefile. You have exceeded maxn
        in the way your datafile.dat is set up. Could be caused by a
        white-space error.

Error Number: 26
Message: Error detected reading pedigree record 200. Liability class 
        (9) exceeds nclass.
What it means: When you specify a locus as as an affection status locus,
         you may specify different liability classes that get numbered
         1,2,3... If you assign an individual a class number in the pedigree
         file that is higher than the number of liability classes
         specified, then error 26 occurs. It is important to remember that
         affection status loci get 1 column is no liability classes are used
         and 2 columns if classes are used. Therefore, this error can occur
         if you specify an affection status locus to have liability classes
         in the locus file, but forget to specify the class in the
         pedigree file.

Error Number: 27
Message: Error detected reading pedigree record 200. Illegal liability
         class (0).
What it means: See error 26. In this case the liability class is being read 
         as a number that is too low (rather than too high), but the likely
         causes are the same as for 26.

Error Number: 28
Message: Error detected reading locus description for system 1. 
         Liability classes (100) exceed maxliab.
What it means: The maximum number of liability classes at a locus is
        determined by the constant maxliab, which can be set in
        unknown.c, commondefs.h, or Makefile.

Error Number: 29
Message: Error detected reading locus description for system 2. 
         Illegal number of liability classes (-1)\n",
What it means: The number of liability classes that you specified for
         an affection status locus is too low. This could be a
         white-space error.

Error Number: 30
Message: Error detected reading locus description for system 2.
         Penetrance out of range"
What it means: You specified a penetrance for a liability class of
         an affection status locus as a number bigger than 1.0. Probably
         a white-space error.

Error Number: 31
Message: Error detected reading locus description for system 2.
         Number of traits (17) exceeds maxtrait
What it means: The maximum number of traits for a quantitative trait
         locus is determined by the constant maxtrait, which can be
         set in unknown.c, commondefs.h, or Makefile.

Error Number: 32
Message: Error detected reading locus description for system 2.
          Number of traits out of range (-1)
What it means: Similar to error 31, but now the number of traits is
         too low. Probably a white-space error.

Error Number: 33
Message: Error detected reading locus description for system 3. 
         Variance must be positive
What it means: You specified a variance for a quantitative trait as
         0 or less. Almost certainly what happened is that a 0
         was read because of a white-space error.

Error Number: 34
Message: Error detected reading locus description for system 2.
         Variance multiplier must be positive
What it means: Similar to error 33.

Error Number: 35
Message: Error detected reading locus description for system 1.
         Risk allele (17) exceeds nallele
What it means: You are doing a risk assessment and you specified an
          allele number that is higher than the number of alleles possible
          for that locus.

Error Number: 36
Message: Error detected reading locus description for system 2. 
         Illegal risk allele (0)
What it means: Similar to 35, but here the risk allele number is 0 or less.
        Probably a white-space error.

Error Number: 37
Message: Error detected reading datafile. Risk locus (5) exceeds nlocus
What it means: The locus at which you want to do a risk analysis
         is specified as an index that is higher than the number
         of loci you specified in the lcp script.

Error Number: 38
Message: Error detected reading datafile. 
         Illegal value for risk locus (0)
What it means: Similar to 37, but now the risk locus number is too low.
         Probably a white-space error.

Error Number: 39
Message: Error detected reading datafile. 
         Mutation locus (5) exceeds nlocus
What it means: Similar to 37, but this occurs when you are using the
         mutation model, rather than risk analysis.

Error Number: 40
Message: Error detected reading datafile. 
         Illegal value for mutation locus (0)
What it means:Similar to 38, but this occurs when you are using the
         mutation model, rather than risk analysis.

Error Number: 41
Message: Error detected reading datafile. 
         Linkage disequilibrium is not allowed with this program
What it means: You are trying to allow for linkage disequilibrium and trying
         to use LODSCORE. Use ILINK instead.

Error Number: 42
Message: Locus 17 in lod score list exceeds nlocus 5
What it means:  Essentially the same as error 2, but you get this
                one if you use LODSCORE because the lcp script format for
                lodscore is different.

Error Number: 43
Message: Illegal locus number 0 in lod score list
What it means: Similar to error 42, but now the locus number is
               too high instead of too low.


Warning number: 0
Message: Illegal sex difference parameter 3 Parameter should be 0, 1, or 2
What it means: The first number after the last locus description in
               the locus file indicates whether you want male theta and
               female theta to be different
               Codes are:
               0 -- no difference (almost everyone uses this)
               1 -- difference, but no females seen yet
               2 -- difference (common value for sex difference)
               This is probably a white-space error

Warning number: 1
Message: Illegal interference parameter 17 Lack of interference assumed
What it means:  The second number after the last locus description in
                the locus file indicates whether you want interference (1)
                or mapping (2). No interference (the common case) is 0.

Warning Number: 2
Message: Illegal sex difference parameter 1 
         Parameter must be 0 with sex-linked data
What it means: You are using X-chromosome data and you specified that
      male theta should be different from female theta in datain.dat.
      This number is the first number after the last locus description
      in the locus file. This warning may be harmless.

Warning Number 3
Message: Non-standard affection status 6 interpreted as normal
         in pedigree record 200
What it means: The affection status of a person can be 0,1, or 2. You probably
         have a white-space error. This warning should not be ignored.


    |*|   Error Message Introduced in  FASTLINK 

Message: WARNING: You are doing an autosomal 
         run but have AUTOSOMAL_RUN set to 0
What it means: Change AUTOSOMAL_RUN to 1 in moddefs.h

Message: You probably need to run the slower version of this program
What it means: FASTLINK can be configure to use more memory "fast version"
         or less memory "slow version". You are using the fast version and have
         run out of memory. Recompile to get the slow version instead, with
          make installslow.

Message:Problem with malloc, probably not enough space
What it means: You are out of memory, get more swap space.

Message: Your pedigree has more loops than allowed by the constant maxloop
What it means: You must increase maxloop in commondefs.h. Starting
      with FASTLINK 3.0P maxloop will occur also in unknown.c
      You are *strongly encouraged* to read loops.ps.

Message: The program will exit politely to allow you to correct the problem
What it means: I am sparing you a core dump

Message: Error opening ipedfile.dat and pedfile.dat.
What it means: Something is wrong in your lcp script or your usage of it

Message: NOTE: attempting to continue previous (unfinished) run
What it means: FASTLINK thinks you want to recover from a crash

Message: Data recovered
What it means: FASTLINK is recovering from a crash whether you like it
               or not.

Message: Illegal instruction (on Suns)
What it means: maxhap is probably too big causing you to blow
        out the stack in segdown or segup


Message: The next pedigree appears to have an unbroken loop
What it means: You failed to use properly the loops program as part of makeped 
         See Chapter 7 of Terwilliger and Ott


      |*|  Incompatibility Errors in UNKNOWN

One of the main purposes of UNKNOWN is to detect violations of Mendelian
rules of inheritance. In LINKAGE and FASTLINK, through version 2.2,
error detection was done only for loopless pedigrees and the program would
report only the erroneous pedigree/locus pair.

In FASTLINK 2.3P, the loopless error checking was improved so that
the program now pinpoints the nuclear family which contains the error.
It is not possible for the program to determine automatically whether it 
is a parent or a child (or both) whose genotype must be changed.

Sometimes, the program will pinpoint multiple nuclear families that are
in error in the same pedigree. In this situation, only the first
nuclear family is sure to be wrong; the others may be propagated
consequences of the first error detected. It may not be possible to
determine whether they are separate errors or not without correcting the
first error. If you want to see the first error only, change the 
default value of the constant ONE_ERROR_ONLY to 1.

In FASTLINK 3.0P, UNKNOWN now detects incompatibility errors in
looped pedigrees. However, it reports only the pedigree/locus pair.
If you wish to have the nuclear families pinpointed, then artificially
remove all the loops by replacing every number that is 2 or higher
in column 9 of the pedigree file with a 0. Then re-run UNKNOWN.
Do not throw away your original pedigree file, since you will want to
fix the genotype errors there and use that file for the actual
computations.

Here are some UNKNOWN-specific error messages:

Message: Reduce max_vectors_considered to 9999
What it means: You have a looped pedigree, probably with multiple
               loops. UNKNOWN is running out of memory keeping track of
               all the possible loop breaker vectors. If you reduce the 
               constant max_vectors_considered you trade space for time.
               The genotype inference for loops becomes less precise, but
               takes less space.

Message: Error opening pedfile.dat in UNKNOWN
What it means: pedfile.dat is not there or you do not have permission
               to read it. This error could arise if you are doing
               multiple runs in the same directory simultaneously
               (this is a no-no for both LINKAGE and FASTLINK) or
               your directory permissions are not set up properly.

Message: foundped() found 0 pedigrees - UNKNOWN
What it means: Something is seriously wrong with pedfile.dat.
               It's hard to imagine what could cause this, but
               the message is in there for safety.


Message: Press <Enter> to continue
What it means: Recent versions of UNKNOWN ask for an interactive response
               when errors occur. This was introduced
               by Terwilliger and Ott. Press <Enter> if you want 
               incompatibilities checked for the remaining pedigrees in your
               data set. Otherwise, kiil the program.


Message: You must increase the constant maxloop
What it means: In FASTLINK 3.0P, maxloop is defined in both unknown.c and
               commondefs.h. In bothe files, the value must be at least
               as large as the number of loops in each pedigree. In
               previous versions of FASTLINK, maxloop appeared only
               in commondefs.h. Edit unknown.c and commondefs.h to
               increase maxloop.

Message: One incompatibility involves the family in which person
         17 is a parent
What it means: You have a violation of Mendelian rules of inheritance in
               the current pedigree. This message will be printed
               before the message for the whole pedigree.
               Here "family" means "nuclear family", including parents
               and children.
               The first nuclear family that is pinpointed definitely has 
               an error (see the introduction to this section. Note that
               the individuals are counted starting at 1 with each pedigree, so
               17 means the 17th person listed in pedfile.dat for the current
               pedigree. Note that if 17 is involved in multiple marriages,
               each of these should be checked.

Message: One incompatibility involves the family in which person
         9 is a child
What it means: Essentially the same as the previous error message, except that
               there are two ways of flagging errors depending on how the
               pedigree is traversed.

Message: The next pedigree appears to have an unbroken loop
What it means: The program is getting into an infinite loop probably because
               you have not broken a loop properly. The LINKAGE preprocessor
               program MAKEPED can be used to break loops before
               running UNKNOWN.

Message: ERROR: Incompatibility detected in this family for locus 2
What it means: This is the overall incompatibility message for a
               pedigree. Here "family" means "pedigree".
               Note that locus 2 here is post-lsp locus numbering.
               so it means the second locus in your analysis.

Message: ERROR: File empty or inconsistent.
What it means: One of pedfile.dat and datafile.dat is not there or
               has the wrong permissions.

      |*|    LSP Error Messages

In many of the following error codes, substituting S for P in the
fifth letter means the problem is in the secondary file, rather than
the primary file. Almost nobody uses secondary files.

Code: LN1RPR
What it means: First line of datain.dat does not have 4 numbers on it
   The 4 numbers are:
     Number of loci Risk locus X-linked Program code

Code: NOLIPR
What it means: Number of loci is lees than 1 or bigger than the
               maximum allowed by lsp.

Code: RKLIPR
What it means: Risk locus is < 0 or bigger than the number of loci
               Risk locus should be 0 unless you want to do a risk
               calculation

Code: XLKIPR
What it means: The X-linked status is something other than 0 (autosomal)
               or 1 (X-linked)

Code: PRGIPR
What it means: Program code is not valid

Code: MPLXPR
What it means: Program code is not valid

Code: NLEXPR
What it means: I wish I knew!

Code: LN2RPR
What it means: There is a problem reading the second line of the locus file
  This should have 4 numbers:
  Mutation locus Male mutation Rate Female Mutation Rate Disequilibrium
  Unless you are a LINKAGE wizard, I *strongly* recommend that this line
  should always be:
  0 0.0 0.0 0

Code: MTLIPR
What it means: Mutation locus is out of range


Code: MMRIPR
What it means: Male mutation rate is out of range

Code: FMRIPR
What it means: Female mutation rate is out of range

Code: MTMXPS
What it means: Mutation locus index is not 0


Code: DISIPR
What it means: Disequilibrium is not 0 or 1

Code: DENXPR
What it means: Disequilibrium is not 0

Code: LN3RPR
What it means: Problem reading the 3 line of locus file that
               specifies the locus order. Usually this means that
               number of entries on this line does not match the
               number of loci specified in the first line of the locus file


Code: LN5RPR
What it means: Problems reading line with sex difference and interference

Code: LN6RPR
What it means: Problems reading line with male recombination fractions

Code: LN7RPR
What it means: Problems reading line with female recombination fractions

Code: LCOIPR
What it means: Entry in locus order is not between 1 and the number of
               loci specified.

Code: SXDIPR
What it means: Problems reading the sex difference entry in the line
               immediately after the last locus, which has two numbers:
               Sex difference Interference

Code: INFIPR
What it means: Problems reading the interference entry, which should be 0, 1
               or 2.

Code: MRFIPR
What it means: Male recombination fraction not in the range [0.0, 1.0]

Code: GDRIPR
What it means: Problems reading either the sex difference ratio

Code: FRFIPR
What it means: Female recombination fraction not in the range [0.0, 1.0]

Code: PNORPP
What it means: Problems reading column 1 entry in pedigree file.
               This is the most common lsp error. It occurs when there
               are extra blanks at the end of the file

Code: IIDRP
What it means: Problems reading column 2 entry in pedigree file.

Code: PIDRP
What it means: Problems reading column 3 entry in pedigree file.

Code: MIDRP
What it means: Problems reading column 4 entry in pedigree file.

Code: FOSRPP
What it means: Problems reading column 5 entry in pedigree file.

Code: NPSRPP
What it means: Problems reading column 6 entry in pedigree file.

Code: NMRSPP
What it means: Problems reading column 7 entry in pedigree file.

Code: SEXRPP
What it means: Problems reading column 8 entry in pedigree file.

Code: PRORPP
What it means: Problems reading column 9 entry in pedigree file.

Code: QANRPP
What it means: Problems reading value for quantitative locus in
               pedigree file. Beware of spurious carriage returns

Code: AFFRPP
What it means: Problems reading affection status entry in pedigree file
               Beware of spurious carriage returns

Code: BINRPP
What it means: Problems reading binary code entry in pedigree file
               Beware of spurious carriage returns

Code: ALERPP
What it means: Problems reading allele entry in pedigree file
               Beware of spurious carriage returns

Code: FLDRPR
What it means: Cannot find two entries on the first line of a locus
               description. First entry is locus type, meaning
               second entry depends on locus type.

Code: LDCIPR
What it means: First entry in a locus description is something other
               than 1,2,3,4

Code: NALIPR
What it means: Second entry of a locus description is < 1

Code: FGFRPR
What it means: Problems finding an allele frequency

Code: GFQIPR
What it means: Allele frequency is not in the open interval (0.0,1.0)
               Beware that Genethon publishes some allele frequencies
               as 0.0

Code: GFSXPR
What it means: Warning if allele frequencies sum to < 0.95 or more than
               1.05

Code: NQVRPR
What it means: Problems reading a quantitative trait locus

Code: NQVIPR
What it means: Number of classes for a quantitative trait locus is < 1

Code: GTMRPR
What it means: Problem reading details of a quantitative trait locus

Code: VARRPR
What it means: Problems reading variance for quantitative trait locus

Code: VARIPR
What it means: A variance component is < 0.0

Code: CVMRPR
What it means: Problems reading a covariance component

Code: VMLRPR
What it means: Something to do with a quantitative trait locus,
               but I don't know what

Code: VMLIPR
What it means:  Something to do with a quantitative trait locus,
               but I don't know what

Code: NLCRPR
What it means: Problems reading number of liability classes for affection
               status

Code: NLCIPR
What it means: Number of liability classes is < 1

Code: GTPRPR
What it means: Problems reading a penetrance

Code: GTPIPR
What it means: A penetrance is not in the range [0.0, 1.0]

Code: NBFRPR
What it means: Problems reading number of factors for a binary
               factors locus

Code: NBFIPR
What it means: Number of factors is < 1

Code: BFCRPR
What it means: Problems reading the meaning of a binary factor combination

Code: BFCIPR
What it means: A binary factor is not 0 or 1


Code: RKAPR
What it means: Problems reading risk allele
 
Code: RKIPR
What it means: Risk allele is < 1

Code: CMDRCI
What it means: Problems parsing the arguments to lsp

Code: CMDOPN
What it means: Cannot open one of the data files or arguments to
               lsp are wrong

Code: PEDRCI
What it means: Not enough arguments to lsp

Code: PEDOPN
What it means: Cannot open one of the data files or arguments to
               lsp are wrong

Code: PARRCI
What it means: Not enough arguments to lsp

Code: PAROPN
What it means: Cannot open one of the data files or arguments to
               lsp are wrong

Code: NOLRCI
What it means: Not enough arguments to lsp

Code: NOLICI
What it means: Number of loci given to lsp is < 2 or too many

Code: LCORCI
What it means: Not enough arguments to lsp

Code: LCOICI
What it means: Invalid locus number in locus order

Code: INFRCI
What it means: Not enough arguments to lsp

Code: INFICI
What it means: Interference value is not 0,1, or 2 in call to lsp

Code: SXDRCI
What it means: Not enough arguments to lsp

Code: SXDICI
What it means: Sex difference argument to lsp is not 0,1, or 2

Code: MRFRCI
What it means: Not enough arguments to lsp

Code: MRFICI
What it means: Male recombination fraction argument to lsp is not
               between 0.0 and 1.0

Code: GDRRCI
What it means: Nor enough arguments to lsp

Code: GDRICI
What it means: Problems reading genetic distance ratio as argument to lsp

Code: FRFRCI
What it means: Not enough arguments to lsp

Code: FRFICI
What it means: Problems reading a female recombination fraction as
               an argument to lsp

Code: CMDPAR 
What it means: Too many arguments to lsp

Code: PDFOPN
What it means: Problems opening pedigree file

Code: DTFOPN
What it means: Problems opening data file

Code: LOGOPN
What it means: Problems opening lsp logfile

Code: STMOPN
What it means: Problems opening stream file


Code: LEPIPR
What it means: I wish I knew

Code: LEPRPR
What it means: You cannot do this with LODSCORE or ILINK

Code: GNPIPR
What it means: Problems with iterated parameters

Code: GNPRPR
What it means: You cannot do this with LODSCORE or ILINK

Code: TLCRCI
What it means: Not enough arguments to lsp

Code: TLCIC
What it means: Locus number is < 1 or too high as argument to lsp

Code: STVRCI
What it means: Not enough arguments to lsp

Code: STVRCI
What it means: Stop value for moving theta is not between 0.0 and 1.0

Code: GRSRCI
What it means: Not enough arguments to lsp

Code: GRSICI
What it means: Number of evaluations in interval or LINKMAP is < 1

Code: RFVRCI
What it means: Not enough arguments to lsp

Code: RFVICI
What it means: For MLINK usage recombination fraction to vary is
               < 1 or > number of loci

Code: INVRCI
What it means: Not enough arguments to lsp

Code: INVICI
What it means: Increment value for MLINK is <= 0.0

Code:NOERCI
What it means: Not enough arguments to lsp

Code: NOEICI
What it means: Number of additional likelihood evaluations for MLINK is  < 0
               or > some specified limit.

Code: IRFRCI
What it means: Not enough arguments to lsp

Code: IRFICI
What it means: Initial recombination fraction for MLINK is not in the
               range [0.0, 1.0]

Code: INTERR
What it means: Internal error in lsp. Heaven help you if you get this code!

Code: CMDNTF
What it means: Lsp does not understand how to set up for this program
               I think you get this if you ask to run a program that is
               not one of the LINKAGE main programs.

Code: CMDNTU
What it means: Similar to CMDNTF. I can't tell the difference.

Code: CMDNOD
What it means: Probably some junk characters in input

Code: SPDRCI
What it means: Looking for name of secondary pedigree file
               and can't find it

Code: SPDOPN
What it means: Problems opening secondary pedigree file

Code: SPRRCI
What it means: Looking for name of secondary locus file and can't find it

Code: SPROPN
What it means: Problems opening secondary locus file

Code: OPDRCI
What it means: Problems finding the name of output pedigree file
               (to use as input to unknown)

Code: OPDOPN
What it means: Problems opening output pedigree file

Code: OPRRCI
What it means: Problems finding the name of output locus file

Code: OPRRCN
What it means: Problems opening output locus file

Code: FTLXSP
What it means: Problems setting up secondary pedigree file

Code: SPEMP
What it means: Individual has index 0

Code: FSKXSP
What it means: Problems with secondary pedigree file

Code: PPDEMP
What it means: Problems reading a pedigree number

Code: PLNRSP
What it means: Problems reading from secondary pedigree file

Code: PNMXPS
What it means: Problems merging primary and secondary pedigree files

Code: INMXPS
What it means: Problems merging primary and secondary pedigree files

Code: FIMXPS
What it means: Problems merging primary and secondary pedigree files


Code: MIMXPS
What it means: Problems merging primary and secondary pedigree files


Code: FOMXPS
What it means: Problems merging primary and secondary pedigree files


Code: NPMXPS
What it means: Problems merging primary and secondary pedigree files


Code: SXMXPS
What it means: Problems merging primary and secondary pedigree files


Code: IIDIPP
What it means: Problems merging primary and secondary pedigree files


Code: PIDIPP
What it means: Problems merging primary and secondary pedigree files

Code: MIDIPP
What it means: Problems merging primary and secondary pedigree files

Code: FOSIPP
What it means: Problems merging primary and secondary pedigree files

Code: NPSIPP
What it means: Problems merging primary and secondary pedigree files

Code: NMSIPP
What it means: Problems merging primary and secondary pedigree files

Code: SEXIPP
What it means: Problems merging primary and secondary pedigree files

Code: PROIPP
What it means: Problems merging primary and secondary pedigree files


      |*|    LRP Error Messages

Message: Screen width is too small
What it means: If you are using a one-window system, there is not much
               you can do. However, if you have control over your windows,
               it may help to widen the window in which you run lrp and
               start over.

Message: Screen length is too small
What it means: Similar to previous message. Try lengthening your window and
               starting over.

Message: Internal Error
What it means: If there is no modifier to describe the Internal Error you
               have hit a bug in lrp.

Message: Internal Error - Length of 'lrp_rprt_scrn' exceeded 
         LRP_MAX_STRING_BUFFER_LENGTH
What it means: You hit a bug in lrp and the authors of the program are 
               protecting you from a core dump.

Message: Internal Error - Length of 'lrp_hlp1_scrn' exceeded 
         LRP_MAX_STRING_BUFFER_LENGTH
What it means: See the previous message

Message: Internal Error - Length of 'lrp_hlp2_scrn' exceeded
         LRP_MAX_STRING_BUFFER_LENGTH
What it means: See the previous message

Message; Internal Error - Length of 'lrp_hlp3_scrn' exceeded
         LRP_MAX_STRING_BUFFER_LENGTH
What it means: See the previous message

Message: Internal Error - Length of 'lrp_help_line' exceeded
         LRP_MAX_STRING_BUFFER_LENGTH
What it means: See the previous message

Message: Internal Error - Length of 'lrp_info_line' exceeded
         LRP_MAX_STRING_BUFFER_LENGTH
What it means: See the previous message

Message: Internal Error - Length of 'lrp_cmmd_line' exceeded
         LRP_MAX_STRING_BUFFER_LENGTH
What it means: See the previous message

Message: Internal Error - Length of 'lrp_wait_line' exceeded
         LRP_MAX_STRING_BUFFER_LENGTH
What it means: See the previous message

Message: Internal Error - Length of 'lrp_vers_line' exceeded
         LRP_MAX_STRING_BUFFER_LENGTH
What it means: See the previous message

Message: Internal Error - Memory allocation failure
What it means: You are out of memory. Look around for other processes that
               may be using all the memory.


Message: Internal Error - Bad field number
What it means: There was a problem in the way you specified the report format


Message: Internal Error - Function FSEEK failed
What it means: There was a problem modifying the report file. If your disk
               is on a different machine, this might be a network problem.

Message Internal Error - Function TMPNAM failed
What it means: I do not know

Message: Internal Error - Function FOPEN failed
What it Means: Could not open the file that you designated as the report file
               Possible reasons include improper permission for the directory
               you are working in or a disk problem.


mutl.c: Internal Error - Function LSF_REWIND failed
What it Means: Could not read from the stream file that you designated.
               Maybe it doesn't exist. Maybe the permission is wrong.
               Maybe there is a disk problem.

mutl.c: Internal Error - Function LSF_STATUS_TEXT failed
What it Means: While attempting to print out an error message, another error
               occurred. I cannot figure out why this would happen, though.

mutl.c: Internal Error - Function LSF_INFORMATION failed
What it Means: While trying to figure out if the stream file was properly
               formatted, an error occurred. This is probably not an
               error with the contents of the stream file, but with
               access to it.

rful.c:	Internal error - LSF_READ error detected
What it Means: Problems reading the contents of your stream file.
               Although the lsf_read routine reports a diagnostic of the
               error, this diagnostic is not used in the error printing
               routine.

rloc.c: Internal error - LSF_ALLOCATE error detected
What it Means: Memory allocation problem

rloc.c:	Internal error - LSF_READ_SET error detected
What it Means: Problems reading the contents of the stream file

ulth.c:	Must specify temporary file name
What it Means: You mangled the file specifications for the input or
               output files. Start over.

ulth.c:	Must specify temporary file name
What it Means: You mangled the file specifications for the input or
               output files. Start over.

ulth.c:	Must specify report file name
What it Means: You mangled the file specifications for the input or
               output files. Start over.

ulth.c:	Must specify stream file name
What it Means: You mangled the file specifications for the input or
               output files. Start over.

ulth.c:	Must specify report title
What it Means: You mangled the file specifications for the input or
               output files. Start over.

