warning message

[sotaro-kanematsu]

I run scarHRD using sequenza *.small.seq.gz as input file, and I got warning message as below.

What's wrong?

scar_score("/run/media/skanematsu/9ce21fae-49c9-4d74-a898-7ac57ac02b29/sequenza/results/WGS/WG0015__WG0016_WG0015__WG0016_tumor/WG0015__WG0016_WG0015__WG0016_tumor.out.small.seqzPreprocessing started...", seqz=TRUE, chr.in.names=FALSE)
Collecting GC information ............................................................................................................................................................................................................ done

Processing 1:
544 variant calls.
374 copy-number segments.
159858 heterozygous positions.
9756090 homozygous positions.
Processing 2:
617 variant calls.
243 copy-number segments.
167178 heterozygous positions.
11252969 homozygous positions.
Processing 3:
339 variant calls.
152 copy-number segments.
151357 heterozygous positions.
8463792 homozygous positions.
Processing 4:
491 variant calls.
257 copy-number segments.
151892 heterozygous positions.
8191443 homozygous positions.
Processing 5:
444 variant calls.
175 copy-number segments.
129249 heterozygous positions.
8348594 homozygous positions.
Processing 6:
435 variant calls.
299 copy-number segments.
137295 heterozygous positions.
7330989 homozygous positions.
Processing 7:
400 variant calls.
282 copy-number segments.
123755 heterozygous positions.
6701081 homozygous positions.
Processing 8:
385 variant calls.
217 copy-number segments.
114530 heterozygous positions.
6202254 homozygous positions.
Processing 9:
296 variant calls.
184 copy-number segments.
92695 heterozygous positions.
4927459 homozygous positions.
Processing 10:
298 variant calls.
230 copy-number segments.
105259 heterozygous positions.
5652674 homozygous positions.
Processing 11:
316 variant calls.
203 copy-number segments.
99418 heterozygous positions.
5739393 homozygous positions.
Processing 12:
306 variant calls.
187 copy-number segments.
95666 heterozygous positions.
5723343 homozygous positions.
Processing 13:
272 variant calls.
124 copy-number segments.
74928 heterozygous positions.
4205669 homozygous positions.
Processing 14:
137 variant calls.
75 copy-number segments.
67596 heterozygous positions.
3625828 homozygous positions.
Processing 15:
188 variant calls.
128 copy-number segments.
63433 heterozygous positions.
3498831 homozygous positions.
Processing 16:
205 variant calls.
132 copy-number segments.
65664 heterozygous positions.
3656314 homozygous positions.
Processing 17:
190 variant calls.
161 copy-number segments.
56260 heterozygous positions.
3437042 homozygous positions.
Processing 18:
227 variant calls.
140 copy-number segments.
57844 heterozygous positions.
3287200 homozygous positions.
Processing 19:
157 variant calls.
147 copy-number segments.
45993 heterozygous positions.
2521251 homozygous positions.
Processing 20:
148 variant calls.
103 copy-number segments.
45145 heterozygous positions.
2629299 homozygous positions.
Processing 21:
109 variant calls.
83 copy-number segments.
35472 heterozygous positions.
1570443 homozygous positions.
Processing 22:
88 variant calls.
96 copy-number segments.
27945 heterozygous positions.
1514616 homozygous positions.
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=11m 52s
Preprocessing finished
Determining HRD-LOH, LST, TAI
HRD Telomeric AI LST HRD-sum
[1,] 4 2 2 8
Warnings:
mean.default(extract$gc$adj[, 2]):
argument is not numeric or logical: returning NA

[VaishnaviKyvor]

I got the same thing. The process doesn't run beyond Chr 7. Please help!!

[jasonthomson7]

I also get the same warning. Can we still trust the scarHRD results if this warning is been shown? Anybody managed to solve the problem? Thanks!

[sigusn]

I have the same issue, stops after chr14...

[s-juross]

I get the same error, did anybody solve it??