Post by snow on Mar 30, 2018 20:32:39 GMT
I have Mach file: cut10.mldose and cut10.mlinfo as following:
-bash-4.1$ more cut10.mldose
2_2->2_2 ML_DOSE 1.195 0.000 0.000 0.000 0.000 0.001 0.001 0.000 0.000 0.007
3_3->3_3 ML_DOSE 1.019 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.001
4_4->4_4 ML_DOSE 1.835 0.002 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.008
5_5->5_5 ML_DOSE 1.959 0.000 0.000 0.000 0.000 0.001 0.001 0.000 0.000 0.001
6_6->6_6 ML_DOSE 1.604 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.003
10_10->10_10 ML_DOSE 1.896 0.000 0.000 0.000 0.000 0.001 0.001 0.000 0.000 0.019
11_11->11_11 ML_DOSE 1.891 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.010
12_12->12_12 ML_DOSE 1.948 0.001 0.000 0.000 0.000 0.004 0.001 0.000 0.000 0.021
15_15->15_15 ML_DOSE 1.946 0.000 0.000 0.000 0.000 0.002 0.002 0.000 0.000 0.006
16_16->16_16 ML_DOSE 1.901 0.030 0.000 0.000 0.000 0.005 0.005 0.000 0.000 0.003
-bash-4.1$ more cut10.mlinfo
SNP Al1 Al2 Freq1 MAF Quality Rsq
11:70864 A G 0.91775 0.08225 0.94428 0.41895
11:115282 C T 0.00061 0.00061 0.99950 0.22275
11:119945 G C 0.00002 0.00002 0.99998 0.09167
11:123302 G A 0.00015 0.00015 0.99985 0.07591
11:123430 G C 0.00007 0.00007 0.99993 0.05161
11:128192 C A 0.00097 0.00097 0.99915 0.18656
11:128196 A G 0.00068 0.00068 0.99937 0.15250
11:128425 G C 0.00007 0.00007 0.99995 0.35735
11:128429 C G 0.00016 0.00016 0.99986 0.20419
11:128882 G A 0.01083 0.01083 0.99136 0.28634
When I run: gcta64 --dosage-mach cut10b.mldose cut10b.mlinfo --make-bed --out cut10.out
I get the information:
Reading map file of the imputed dosage data from [cut10b.mlinfo].
Reading dosage data failed. Please check the format of the map file.
Are there something wrong? any suggestion? Thank you so much.
-bash-4.1$ more cut10.mldose
2_2->2_2 ML_DOSE 1.195 0.000 0.000 0.000 0.000 0.001 0.001 0.000 0.000 0.007
3_3->3_3 ML_DOSE 1.019 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.001
4_4->4_4 ML_DOSE 1.835 0.002 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.008
5_5->5_5 ML_DOSE 1.959 0.000 0.000 0.000 0.000 0.001 0.001 0.000 0.000 0.001
6_6->6_6 ML_DOSE 1.604 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.003
10_10->10_10 ML_DOSE 1.896 0.000 0.000 0.000 0.000 0.001 0.001 0.000 0.000 0.019
11_11->11_11 ML_DOSE 1.891 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.010
12_12->12_12 ML_DOSE 1.948 0.001 0.000 0.000 0.000 0.004 0.001 0.000 0.000 0.021
15_15->15_15 ML_DOSE 1.946 0.000 0.000 0.000 0.000 0.002 0.002 0.000 0.000 0.006
16_16->16_16 ML_DOSE 1.901 0.030 0.000 0.000 0.000 0.005 0.005 0.000 0.000 0.003
-bash-4.1$ more cut10.mlinfo
SNP Al1 Al2 Freq1 MAF Quality Rsq
11:70864 A G 0.91775 0.08225 0.94428 0.41895
11:115282 C T 0.00061 0.00061 0.99950 0.22275
11:119945 G C 0.00002 0.00002 0.99998 0.09167
11:123302 G A 0.00015 0.00015 0.99985 0.07591
11:123430 G C 0.00007 0.00007 0.99993 0.05161
11:128192 C A 0.00097 0.00097 0.99915 0.18656
11:128196 A G 0.00068 0.00068 0.99937 0.15250
11:128425 G C 0.00007 0.00007 0.99995 0.35735
11:128429 C G 0.00016 0.00016 0.99986 0.20419
11:128882 G A 0.01083 0.01083 0.99136 0.28634
When I run: gcta64 --dosage-mach cut10b.mldose cut10b.mlinfo --make-bed --out cut10.out
I get the information:
Reading map file of the imputed dosage data from [cut10b.mlinfo].
Reading dosage data failed. Please check the format of the map file.
Are there something wrong? any suggestion? Thank you so much.