Troubleshooting Error Codes Reported by LSP

BioInformatics & Molecular Analysis Section, CIT, NIH

Presented in the following table are the LSP error codes in alphabetical order, along with the common causes. This information is derived from the Linkage Troubleshooting Guide by Dr. Alejando Schaffer, NHGRI.

Note: 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. Secondary files are used very infrequently.

Table of Common Reasons for LSP Errors
LSP Code Common Cause
AFFRPP Problems reading affection status entry in pedigree file. Beware of spurious carriage returns.
ALERPP Problems reading allele entry in pedigree file. Beware of spurious carriage returns.
BFCIPR A binary factor is not 0 or 1
BFCRPR Problems reading the meaning of a binary factor combination
BINRPP Problems reading binary code entry in pedigree file. Beware of spurious carriage returns.
CMDNOD lsp requires the first argument to match it's internal command table. This argument appeared to be NULL. Beware of spurious carriage returns.
CMDNTF lsp requires the first argument to match it's internal command table. The argument was not found in lsp's internal command table.
CMDNTU lsp requires the first argument to match it's internal command table. The argument was to short - it was found in the table, but to short to be unique. Example: CM which could be CMAP or CMLINK.
CMDOPN Cannot open one of the data files or arguments to lsp are wrong
CMDPAR Too many arguments to lsp
CMDRCI Problems parsing the arguments to lsp
CVMRPR Problems reading a covariance component
DENXPR Disequilibrium is not 0
DISIPR Disequilibrium is not 0 or 1
DTFOPN Problems opening data file
FGFRPR Problems finding an allele frequency
FIMXPS Problems merging primary and secondary pedigree files
FLDRPR Cannot find two entries on the first line of a locus description. First entry is locus type, meaning second entry depends on locus type.
FMRIPR Female mutation rate is out of range
FOMXPS Problems merging primary and secondary pedigree files
FOSIPP Problems merging primary and secondary pedigree files
FOSRPP Problems reading column 5 entry in pedigree file.
FRFICI Problems reading a female recombination fraction as an argument to lsp
FRFIPR Female recombination fraction not in the range [0.0, 1.0]
FRFRCI Not enough arguments to lsp
FSKXSP Problems with secondary pedigree file
FTLXSP Problems setting up secondary pedigree file
GDRICI Problems reading genetic distance ratio as argument to lsp
GDRIPR Problems reading either the sex difference ratio
GDRRCI Not enough arguments to lsp
GFQIPR Allele frequency is not in the open interval (0.0,1.0) Beware that Genethon publishes some allele frequencies as 0.0
GFSXPR Warning if allele frequencies sum to < 0.95 or more than 1.05
GNPIPR Problems with iterated parameters
GNPRPR You cannot do this with LODSCORE or ILINK
GRSICI Number of evaluations in interval or LINKMAP is < 1
GRSRCI Not enough arguments to lsp
GTMRPR Problem reading details of a quantitative trait locus
GTPIPR A penetrance is not in the range [0.0, 1.0]
GTPRPR Problems reading a penetrance
IIDIPP Problems merging primary and secondary pedigree files
IIDRP Problems reading column 2 entry in pedigree file.
INFICI Interference value is not 0,1, or 2 in call to lsp
INFIPR Problems reading the interference entry, which should be 0, 1 or 2.
INFRCI Not enough arguments to lsp
INMXPS Problems merging primary and secondary pedigree files
INTERR Internal error in lsp. Heaven help you if you get this code!
INVICI Increment value for MLINK is <= 0.0
INVRCI Not enough arguments to lsp
IRFICI Initial recombination fraction for MLINK is not in the range [0.0, 1.0]
IRFRCI Not enough arguments to lsp
LCOICI Invalid locus number in locus order
LCOIPR Entry in locus order is not between 1 and the number of loci specified.
LCORCI Not enough arguments to lsp
LDCIPR First entry in a locus description is something other than 1,2,3,4
LEPIPR I wish I knew
LEPRPR You cannot do this with LODSCORE or ILINK
LN1RPR 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
LN2RPR 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
LN3RPR 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
LN5RPR Problems reading line with sex difference and interference
LN6RPR Problems reading line with male recombination fractions
LN7RPR Problems reading line with female recombination fractions
LOGOPN Problems opening lsp logfile
MIDIPP Problems merging primary and secondary pedigree files
MIDRP Problems reading column 4 entry in pedigree file.
MIMXPS Problems merging primary and secondary pedigree files
MMRIPR Male mutation rate is out of range
MPLXPR Program code is not valid
MRFICI Male recombination fraction argument to lsp is not between 0.0 and 1.0
MRFIPR Male recombination fraction not in the range [0.0, 1.0]
MRFRCI Not enough arguments to lsp
MTLIPR Mutation locus is out of range
MTMXPS Mutation locus index is not 0
NALIPR Second entry of a locus description is < 1
NBFIPR Number of factors is < 1
NBFRPR Problems reading number of factors for a binary factors locus
NLCIPR Number of liability classes is < 1
NLCRPR Problems reading number of liability classes for affection status
NLEXPR I wish I knew!
NMRSPP Problems reading column 7 entry in pedigree file.
NMSIPP Problems merging primary and secondary pedigree files
NOEICI Number of additional likelihood evaluations for MLINK is < 0 or > some specified limit.
NOERCI Not enough arguments to lsp
NOLICI Number of loci given to lsp is < 2 or too many
NOLIPR Number of loci is lees than 1 or bigger than the maximum allowed by lsp.
NOLRCI Not enough arguments to lsp
NPMXPS Problems merging primary and secondary pedigree files
NPSIPP Problems merging primary and secondary pedigree files
NPSRPP Problems reading column 6 entry in pedigree file.
NQVIPR Number of classes for a quantitative trait locus is < 1
NQVRPR Problems reading a quantitative trait locus
OPDOPN Problems opening output pedigree file
OPDRCI Problems finding the name of output pedigree file (to use as input to unknown)
OPRRCI Problems finding the name of output locus file
OPRRCN Problems opening output locus file
PAROPN Cannot open one of the data files or arguments to lsp are wrong
PARRCI Not enough arguments to lsp
PDFOPN Problems opening pedigree file
PEDOPN Cannot open one of the data files or arguments to lsp are wrong
PEDRCI Not enough arguments to lsp
PIDIPP Problems merging primary and secondary pedigree files
PIDRP Problems reading column 3 entry in pedigree file.
PLNRSP Problems reading from secondary pedigree file
PNMXPS Problems merging primary and secondary pedigree files
PNORPP 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
PPDEMP Problems reading a pedigree number
PRGIPR Program code is not valid
PROIPP Problems merging primary and secondary pedigree files
PRORPP Problems reading column 9 entry in pedigree file.
QANRPP Problems reading value for quantitative locus in pedigree file. Beware of spurious carriage returns.
RFVICI For MLINK usage recombination fraction to vary is < 1 or > number of loci
RFVRCI Not enough arguments to lsp
RKAPR Problems reading risk allele
RKIPR Risk allele is < 1
RKLIPR Risk locus is < 0 or bigger than the number of loci Risk locus should be 0 unless you want to do a risk calculation
SEXIPP Problems merging primary and secondary pedigree files
SEXRPP Problems reading column 8 entry in pedigree file.
SPDOPN Problems opening secondary pedigree file
SPDRCI Looking for name of secondary pedigree file and can't find it
SPEMP Individual has index 0
SPROPN Problems opening secondary locus file
SPRRCI Looking for name of secondary locus file and can't find it
STMOPN Problems opening stream file
STVICI Stop value for moving theta is not between 0.0 and 1.0
STVRCI Not enough arguments to lsp. Beware of spurious carriage returns.
SXDICI Sex difference argument to lsp is not 0,1, or 2
SXDIPR Problems reading the sex difference entry in the line immediately after the last locus, which has two numbers: Sex difference Interference
SXDRCI Not enough arguments to lsp
SXMXPS Problems merging primary and secondary pedigree files
TLCIC Locus number is < 1 or too high as argument to lsp
TLCRCI Not enough arguments to lsp
VARIPR A variance component is < 0.0
VARRPR Problems reading variance for quantitative trait locus
VMLIPR Something to do with a quantitative trait locus, but I don't know what
VMLRPR Something to do with a quantitative trait locus, but I don't know what
XLKIPR The X-linked status is something other than 0 (autosomal) or 1 (X-linked)