In params.tx file, Log-likelihood gets set to NA

[benbfly]

I have a number of samples where Log-likelihood in the params.txt gets set to "NA". Have you seen this before? I am attaching the command run and output text for one of the examples where it gets set to NA. Have you seen this before?

ichor_loglik_na_output_cmd.txt
ichor_loglik_na_output.txt

ichorCNA/R/output.R

Line 132 in 11b58b3

write.table(paste0("Log-likelihood:\t", format(as.numeric(hmmResults$results$loglik[i, "loglik"]), digits=4)), file = fc, col.names = FALSE, row.names = FALSE, quote = FALSE, sep = "\t")

A couple examples that get "NA" (command and output attached for the first sample):

Gender:	unknown
Tumor Fraction:	0.02015
Ploidy:	2.01
Subclone Fraction:	NA
Fraction Genome Subclonal:	0
Fraction CNA Subclonal:	0
Coverage:	NA
ChrY coverage fraction:	NA
Likelihood model:	t
Student's t mean: -0.01, -1e-04, 0.0099, 0.02, 0.03
Student's t precision: 83, 99, 91, 100, 1.4
Gamma Rate Init:	0.049
GC-Map correction MAD:	0.1919
Log-likelihood:	NA


n_0	phi_0	n_est	phi_est	Frac_genome_subclonal	Frac_CNA_subclonal	loglik
0.2	2	1	1.987	0	0	667.9
0.3	2	1	1.985	0	0	667.9
0.4	2	0.98	1.997	0	0	683
0.5	2	0.98	2.01	0	0	683.1
0.6	2	0.98	2.011	0	0	683.1
0.7	2	0.98	2.018	0	0	683.1
0.8	2	0.98	2.009	0	0	683.1
0.9	2	0.98	2.02	0	0	683.1
0.95	2	0.98	2.026	0	0	683.1

Gender:	unknown
Tumor Fraction:	0.02256
Ploidy:	1.178
Subclone Fraction:	NA
Fraction Genome Subclonal:	0
Fraction CNA Subclonal:	0
Coverage:	NA
ChrY coverage fraction:	NA
Likelihood model:	t
Student's t mean: -0.002, 0.0093, 0.021, 0.032, 0.043
Student's t precision: 150, 1000, 30, 29, 1.9
Gamma Rate Init:	0.035
GC-Map correction MAD:	0.03848
Log-likelihood:	NA


n_0	phi_0	n_est	phi_est	Frac_genome_subclonal	Frac_CNA_subclonal	loglik
0.2	2	1	1.977	0	0	2331
0.3	2	1	1.974	0	0	2331
0.4	2	1	1.97	0	0	2331
0.5	2	1	1.964	0	0	2331
0.6	2	1	1.955	0	0	2331
0.7	2	1	1.939	0	0	2331
0.8	2	0.98	1.178	0	0	2336
0.9	2	0.99	0.8699	0	0	2334
0.95	2	0.99	0.8418	0	0	2333

And a couple with ties that don't get NA:

Gender:	unknown
Tumor Fraction:	0.9486
Ploidy:	1.992
Subclone Fraction:	NA
Fraction Genome Subclonal:	0
Fraction CNA Subclonal:	0
Coverage:	NA
ChrY coverage fraction:	NA
Likelihood model:	t
Student's t mean: -0.64, 0.004, 0.39, 0.67, 0.89
Student's t precision: 110, 1100, 290, 24, 1.6
Gamma Rate Init:	0.042
GC-Map correction MAD:	0.04502
Log-likelihood:	2298


n_0	phi_0	n_est	phi_est	Frac_genome_subclonal	Frac_CNA_subclonal	loglik
0.2	2	0.051	1.992	0	0	2312
0.3	2	0.052	1.992	0	0	2312
0.4	2	0.53	1.983	0	0	2298
0.5	2	0.53	1.983	0	0	2298
0.6	2	0.53	1.983	0	0	2298
0.7	2	0.53	1.983	0	0	2298
0.8	2	0.53	1.983	0	0	2298
0.9	2	0.68	1.975	0	0	2251
0.95	2	0.68	1.975	0	0	2251

Gender:	unknown
Tumor Fraction:	0
Ploidy:	1.976
Subclone Fraction:	NA
Fraction Genome Subclonal:	0
Fraction CNA Subclonal:	NaN
Coverage:	NA
ChrY coverage fraction:	NA
Likelihood model:	t
Student's t mean: -0.53, 0.01, 0.36, 0.62, 0.82
Student's t precision: 28, 960, 28, 28, 1.9
Gamma Rate Init:	0.035
GC-Map correction MAD:	0.05052
Log-likelihood:	2271


n_0	phi_0	n_est	phi_est	Frac_genome_subclonal	Frac_CNA_subclonal	loglik
0.2	2	1	1.976	0	0	2271
0.3	2	1	1.973	0	0	2271
0.4	2	1	1.968	0	0	2271
0.5	2	1	1.962	0	0	2271
0.6	2	1	1.952	0	0	2271
0.7	2	1	1.936	0	0	2271
0.8	2	1	1.904	0	0	2271
0.9	2	1	1.807	0	0	2271
0.95	2	1	1.615	0	0	2271