mlink runtime errors occurred #45
Description
when I perform the linkage analysis this error occurred and all the LOD score in the report were 0.
seqlink --vcf fam1.vcf.gz --chrom-prefix 3 --fam fam_w_1.fam --run-linkage --theta-inc 0.05 -K 0.02 --moi AD -M 0.99 -W 0
LOG:
MESSAGE: Binary trait detected in [/mnt/rd01/home/fam_w_1.fam]
MESSAGE: Checking local resources 5/5 ...
MESSAGE: 3 samples found in [/mnt/rd01/home/fam1.vcf.gz]
MESSAGE: 1 families with a total of 3 samples will be scanned for 28,488 pre-defined units
MESSAGE: 624 units (from 207,890 variants) processed; 131 Mendelian inconsistencies and 0 recombination events handled
MESSAGE: 6,489 tri-allelic loci were ignored
MESSAGE: 27,070 units ignored due to absence in VCF file
MESSAGE: 794 units ignored due to absence of variation in samples
MESSAGE: Archiving regional marker data to directory [cache]
MESSAGE: 624 units will be converted to LINKAGE format
MESSAGE: 624 units successfully converted to LINKAGE format
MESSAGE: Archiving LINKAGE format to directory [cache]
MESSAGE: Running linkage analysis ...
MESSAGE: Linkage analysis succesfully performed for 624 units
MESSAGE: 11 "mlink" runtime errors occurred
MESSAGE: Report for [fam1chr3] is generated in HTML format
morever: is both Maternal and Paternal ID necessary for a linkage analysis?when I type in 0 for the sample whose one of the parents were not in the pedigree, it alerts that can't find the parents.
thank you!