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browning-lab / hap-ibd

The hap-ibd program detects identity-by-descent segments in phased genotype data.
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Error: Genetic map has only one map position #8

Closed XIAO2Mark closed 2 years ago

XIAO2Mark commented 2 years ago

Hi, Greeting! I got some problems when i run hap-ibd, may i ask if you can help me to check it? details as bellow,

Copyright (C) 2019 Brian L. Browning Enter "java -jar hap-ibd.jar" to print a list of command line arguments

Program : hap-ibd.jar [ version 1.0, 20May22.818 ] Start Time : 09:26 PM HKT on 26 Sep 2022 Max Memory : 30688 MB

Parameters gt : phased_all_filtered_snp.vcf.gz map : phased_snp.map out : hap-ibd.out min-seed : 2.0 max-gap : 1000 min-extend : 1.0 min-output : 2.0 min-markers : 100 min-mac : 2 nthreads : 48

Exception in thread "main" java.lang.IllegalArgumentException: Genetic map has only one map position: 1 chr1:17397 0 17397 at vcf.PlinkGenMap.fillMapPositions(PlinkGenMap.java:86) at vcf.PlinkGenMap.(PlinkGenMap.java:52) at vcf.PlinkGenMap.fromPlinkMapFile(PlinkGenMap.java:116) at vcf.GeneticMap.geneticMap(GeneticMap.java:119) at hapibd.PbwtIbdDriver.detectIbd(PbwtIbdDriver.java:66) at hapibd.HapIbdMain.main(HapIbdMain.java:77)

many thanks.

browning-lab commented 2 years ago

Hello, First, try to diagnose the problem from the error message.  In this case, the error message explains why the program stopped running.  If you are unable to resolve the problem from the error message, please read the paper describing the hap-ibd method to understand how the method works.  If neither of these steps solves the problem, please contact the author (me) by e-mail (not through the GitHub issues channel), and I will try to help.