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.
| 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) |