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JoinSingles: Cannot load map file generated by SeparateChromosomes

2018-01-30
2018-03-06
  • Jose Andres

    Jose Andres - 2018-01-30

    Hi there,
    I have managed to group my markers into LGs and I now want to "join singles" but my JoinSingles command line cannot upload the map file (SeparateChromosomes output). The map file is in the directory from which I am running the module and I can open it with my text editor. See pasted. Any suggestions?
    Thanks

    dhcp-ccc-5161:LepMap2_binary_and_code Jose$ ls
    COPYING bin paternal_separateChromosomes_30June18
    LDmap_with_Joinsingles_LOD5_30Jan18 bothparents_separateChromosomes_30June18_LOD10 paternal_separateChromosomes_30June182
    LDmap_with_Joinsingles_LOD5_30Jan18.out data1.linkage paternal_separateChromosomes_30June18_LOD2
    Ldis_LepMap2_filter_30Jan18.out maternal_separateChromosomes_30June18_LOD10 paternal_separateChromosomes_30June18_LOD5
    Ldis_Ppedin_29Jan18.txt maternal_separateChromosomes_30June18_LOD8 paternal_separateChromosomes_30June18_LOD8
    Ldis_Ppedin_noGparents_29Jan18.txt paternal_LGjoinedSingles_30Jan18 src
    Ldis_noGparents_LepMap2_filter_30Jan18.out paternal_LGjoinedSingles_LOD5_30Jan18 testing.out
    README paternal_LOD5_30Jan18.txt

    dhcp-ccc-5161:LepMap2_binary_and_code Jose$ java -cp bin/ JoinSingles chromosome_map_file=paternal_LOD5_30Jan18.txt data=Ldis_noGparents_LepMap2_filter_30Jan18.out informativeMask=1 >LDmap_Joinsingles_LOD5_30Jan18


    Mendel error statistics:
    0->0 : 0
    0->1 : 0
    0->2 : 0
    Error rate = 0.0
    1->0 : 0
    1->1 : 0
    1->2 : 0
    Error rate = 0.0
    2->0 : 0
    2->1 : 0
    2->2 : 629
    Error rate = 0.0
    0,2->0,2 : 29236
    0,2->1 : 0
    1,2->1,2 : 33605
    1,2->0 : 0
    Error rate = 0.0


    Filtering markers based on segregation distortion
    Removed 0 markers from family FAM1
    Maternally informative markers = 634 (of 2595)
    Paternally informative markers = 688
    Maternally or paternally informative markers = 865


    Error: unable to load chromosome map file

     
  • Pasi Rastas

    Pasi Rastas - 2018-03-06

    Dear Jose,

    Sorry for taking time to aswer. I only rarely visit Lep-MAP2 discussion anymore.

    The problem is in you command, just remove "chromosome_map_file=" from the command, i.e.

    java -cp bin/ JoinSingles paternal_LOD5_30Jan18.txt ....

    Cheers,
    Pasi

     

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