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
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
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