failed to run segmentation

[asmariyaz23]

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

[valeu]

Dear friend,
can you exclude there short chromosomes from the analysis? For instance, you can only keep chr1-chrY in the chromosome length file. Then, FREEC will not use other (short unassembled) chromosome files like these 14_CL000 etc.
Best wishes
Valentina