sztup / scarHRD

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ERROR of scar_score #26

Open baekip opened 1 year ago

baekip commented 1 year ago

I'm using the tool (scarHRD) you developed, but I can't solve it because of the error message. Other samples do not have issues, but only one sample does not proceed with the error message shown below. I would really appreciate it if you could tell me how to solve it. This sample is a sample that has more mutations than other samples. I would like to refer to it. Best Regards.

score <- scar_score (seq.file, 
                     reference = "grch37",
                     chr.in.name = FALSE,
                     seqz=TRUE)

Error Message

Preprocessing started...
Collecting GC information .............................................................................................................................. done

Processing 1:
   54296 variant calls.
   865 copy-number segments.
   170822 heterozygous positions.
   6090996 homozygous positions.
Processing 2:
   117284 variant calls.
   1629 copy-number segments.
   174767 heterozygous positions.
   7265508 homozygous positions.
Processing 3:
   96222 variant calls.
   1248 copy-number segments.
   152559 heterozygous positions.
   5716194 homozygous positions.
Processing 4:
   106524 variant calls.
   1354 copy-number segments.
   161308 heterozygous positions.
   5742369 homozygous positions.
Processing 5:
   96567 variant calls.
   1086 copy-number segments.
   130998 heterozygous positions.
   5684501 homozygous positions.
Processing 6:
   66154 variant calls.
   1351 copy-number segments.
   146514 heterozygous positions.
   4446091 homozygous positions.
Processing 7:
   72779 variant calls.
   1124 copy-number segments.
   136465 heterozygous positions.
   4477575 homozygous positions.
Processing 8:
   69686 variant calls.
   1013 copy-number segments.
   116426 heterozygous positions.
   4138932 homozygous positions.
Processing 9:
   49857 variant calls.
   815 copy-number segments.
   106605 heterozygous positions.
   3265619 homozygous positions.
Processing 10:
   33108 variant calls.
   914 copy-number segments.
   117085 heterozygous positions.
   3314602 homozygous positions.
Processing 11:
   47075 variant calls.
   1030 copy-number segments.
   104890 heterozygous positions.
   3470945 homozygous positions.
Processing 12:
   49337 variant calls.
   923 copy-number segments.
   98882 heterozygous positions.
   3569681 homozygous positions.
Processing 13:
   53195 variant calls.
   631 copy-number segments.
   77144 heterozygous positions.
   2847099 homozygous positions.
Processing 14:
   5800 variant calls.
   340 copy-number segments.
   69161 heterozygous positions.
   2114784 homozygous positions.
Processing 15:
   39846 variant calls.
   557 copy-number segments.
   65863 heterozygous positions.
   2290936 homozygous positions.
Processing 16:
   30577 variant calls.
   551 copy-number segments.
   76606 heterozygous positions.
   2171227 homozygous positions.
Processing 17:
   17017 variant calls.
   494 copy-number segments.
   56532 heterozygous positions.
   2058491 homozygous positions.
Processing 18:
   46878 variant calls.
   691 copy-number segments.
   59575 heterozygous positions.
   2435681 homozygous positions.
Processing 19:
   9118 variant calls.
   350 copy-number segments.
   48231 heterozygous positions.
   1479047 homozygous positions.
Processing 20:
   23453 variant calls.
   469 copy-number segments.
   54373 heterozygous positions.
   1712294 homozygous positions.
Processing 21:
   13865 variant calls.
   374 copy-number segments.
   40845 heterozygous positions.
   948099 homozygous positions.
Processing 22:
   5169 variant calls.
   302 copy-number segments.
   30691 heterozygous positions.
   868607 homozygous positions.

  |                                                  | 0 % ~calculating  Error in if (!is.na(mat[x, ]$Bf) & !is.na(mat[x, ]$sd.Bf/sqrt(mat[x, ]$weight.Bf))) { : 
  argument is of length zero
s-juross commented 6 months ago

I'm having the exact same error. Did you solve it?