Hello,
I am running ControlFREEC and run into failed to run segmentation errors. Could you please help me understand the issue?
Command output:
1 0.210723
2 0.466443
3 0.183177
4 0.0678733
5 0.0338588
6 0.0168545
7 0.00568308
8 0.00547053
9 0.00116527
10 0.000710966
11 0.000559905
12 0.000436479
13 0.000180124
14 0.000605781
15 0.00190496
16 0.000287085
17 0.000240757
18 0.000729496
19 0.000204649
22 7.18788e-05
23 5.38887e-05
24 5.99443e-05
25 0.000247502
26 5.37563e-05
28 2.66472e-05
29 0.000530215
32 0.000123164
33 5.00402e-05
34 3.1092e-05
36 4.20115e-05
43 2.41678e-05
Seeking eventual subclones...-> Done!
Total proportion of unexplained regions: 84584 out of 232131 = 0.36438
Ploidy RSS score Percentage of Genome Explained
2 2.43925 0.63562
..Best ploidy set to 2 according to the RSS score
..Best ploidy could have been set to 2 according to the percentage of the copy number changes explained by a model with a given ploidy
..Adding BAF info to the Sample dataset
..Calculate BAF per window for chr1
..Total Number of SNPs: 10835422
..Calculate BAF per window for chr10
..Total Number of SNPs: 6507010
..Calculate BAF per window for chr11
..Total Number of SNPs: 6757138
..Calculate BAF per window for chr12
..Total Number of SNPs: 6446281
..Calculate BAF per window for chr13
..Total Number of SNPs: 4579896
..Calculate BAF per window for chr14
..Total Number of SNPs: 4370297
..failed to run segmentation on chr1_KI270706v1_random
..failed to run segmentation on chr1_KI270711v1_random
..failed to run segmentation on chr4_GL000008v2_random
..failed to run segmentation on chr14_GL000009v2_random
..failed to run segmentation on chrUn_KI270742v1
..failed to run segmentation on chr1_KI270766v1_alt
..failed to run segmentation on chr14_KI270846v1_alt
..failed to run segmentation on chr15_KI270851v1_alt
..failed to run segmentation on chr17_KI270857v1_alt
..failed to run segmentation on chr19_KI270938v1_alt
An error occurred in GenomeCopyNumber::addBAFinfo: could not find an SNP index for 14_GL000009v2_random
Hello,
I am running ControlFREEC and run into failed to run segmentation errors. Could you please help me understand the issue?