issues with Processing chrY

[duanshumeng]

[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
[mpileup] 1 samples in 1 input files
Collecting GC information ............................................................................... done

Processing chr1:
2694 variant calls.
355 copy-number segments.
174377 heterozygous positions.
3535919 homozygous positions.
Processing chr2:
2675 variant calls.
434 copy-number segments.
185981 heterozygous positions.
3462374 homozygous positions.
Processing chr3:
2002 variant calls.
636 copy-number segments.
161175 heterozygous positions.
3032613 homozygous positions.
Processing chr4:
2061 variant calls.
238 copy-number segments.
164571 heterozygous positions.
2642838 homozygous positions.
Processing chr5:
1914 variant calls.
429 copy-number segments.
140817 heterozygous positions.
2664844 homozygous positions.
Processing chr6:
54216 variant calls.
315 copy-number segments.
94488 heterozygous positions.
2571966 homozygous positions.
Processing chr7:
2472 variant calls.
293 copy-number segments.
134383 heterozygous positions.
3178129 homozygous positions.
Processing chr8:
1986 variant calls.
637 copy-number segments.
120658 heterozygous positions.
2342417 homozygous positions.
Processing chr9:
1364 variant calls.
257 copy-number segments.
104164 heterozygous positions.
1760848 homozygous positions.
Processing chr10:
1119 variant calls.
281 copy-number segments.
113969 heterozygous positions.
1883859 homozygous positions.
Processing chr11:
906 variant calls.
326 copy-number segments.
107182 heterozygous positions.
1737474 homozygous positions.
Processing chr12:
1272 variant calls.
336 copy-number segments.
104163 heterozygous positions.
1829704 homozygous positions.
Processing chr13:
740 variant calls.
174 copy-number segments.
76344 heterozygous positions.
1230465 homozygous positions.
Processing chr14:
1337 variant calls.
156 copy-number segments.
70741 heterozygous positions.
1614775 homozygous positions.
Processing chr15:
913 variant calls.
107 copy-number segments.
67094 heterozygous positions.
1268897 homozygous positions.
Processing chr16:
35014 variant calls.
46 copy-number segments.
34378 heterozygous positions.
1459538 homozygous positions.
Processing chr17:
796 variant calls.
207 copy-number segments.
65068 heterozygous positions.
1193466 homozygous positions.
Processing chr18:
729 variant calls.
151 copy-number segments.
63508 heterozygous positions.
1174898 homozygous positions.
Processing chr19:
615 variant calls.
61 copy-number segments.
54666 heterozygous positions.
893063 homozygous positions.
Processing chr20:
899 variant calls.
67 copy-number segments.
61025 heterozygous positions.
1021553 homozygous positions.
Processing chr21:
271 variant calls.
25 copy-number segments.
37636 heterozygous positions.
443041 homozygous positions.
Processing chr22:
609 variant calls.
131 copy-number segments.
40940 heterozygous positions.
720292 homozygous positions.
Processing chrX:
25209 variant calls.
7 copy-number segments.
2224 heterozygous positions.
1669982 homozygous positions.
Warning message:
In (function (..., deparse.level = 1) :
number of columns of result is not a multiple of vector length (arg 1523)
Error in [<-.data.frame(*tmp*, tmp[, 8] > tmp[, 7], 7, value = c(1L, :
missing values are not allowed in subscripted assignments of data frames
Calls: scar_score -> preprocess.hrd -> [<- -> [<-.data.frame
Execution halted