Error in segmenting depth ratios

[Kwon Kujin]

Hello, I'm trying to identify tumor purity from Strelka2 vcf output. 
Due to error issues in GC information collections, I installed packages downloaded from sequenza bitbucket chemins branch (ref. https://groups.google.com/g/sequenza-user-group/c/UA5bBNBeN18)

When I ran sequenza.extract( ) with seqz files generated from Strelka2 SNV (pass) vcf files, I got error messages below
Collecting GC information . done

Collecting BAF/ratio information . done
Processing chr1:
Segmenting depth ratios
Error: upper value must be greater than lower value

 
I also generated seqz files with non-filtered Strelka2 SNV vcf files, I successfully proceed to segmentation process but I got the same error in chrY process.

Is there any recommendation to solve this error?

One more thing is that I only got 1 variant calls from chr1 to chrX process. Is it okay to change min.fw.freq from 0 to NA? (ref. https://groups.google.com/g/sequenza-user-group/c/S-aEOtWFny8/m/lRi77YZOAAAJ)

sessionInfo:
R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS/LAPACK: /home/project1/lab/kkwon/mambaforge/envs/r_version3/lib/libopenblasp-r0.3.26.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=ko_KR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=ko_KR.UTF-8    LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=ko_KR.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=ko_KR.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] sequenza_3.0.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.12        pracma_2.4.4       pillar_1.9.0       compiler_4.2.2    
 [5] ks_1.14.2          iotools_0.3-5      tools_4.2.2        mclust_6.1        
 [9] bit_4.0.5          lifecycle_1.0.4    tibble_3.2.1       lattice_0.22-5    
[13] pkgconfig_2.0.3    rlang_1.1.3        Matrix_1.6-5       cli_3.6.2        
[17] curl_4.3.3         parallel_4.2.2     mvtnorm_1.2-4      withr_3.0.0      
[21] dplyr_1.1.4        stringr_1.5.1      generics_0.1.3     vctrs_0.6.5      
[25] hms_1.1.3          bit64_4.0.5        grid_4.2.2         tidyselect_1.2.0  
[29] glue_1.7.0         R6_2.5.1           fansi_1.0.6        pbapply_1.7-2    
[33] vroom_1.6.5        seqminer_9.4       tzdb_0.4.0         readr_2.1.5      
[37] magrittr_2.0.3     utf8_1.2.4         squash_1.0.9       KernSmooth_2.23-22
[41] stringi_1.8.3      crayon_1.5.2

Thanks,
Kujin