Solved: The file names contained "_", which was cut off at some point during "seGMM". Switching "_" to "-" solved the issue.
There appears to be an error in the clustering. It worked for lower sample sizes. Now I have 649 samples and I get this error:
$ seGMM -vcf P1823_vardict.vcf.gz -i P1823_files.txt -R genome.fasta -g hg38 -a BAM -t TGS -c x -s False -n 20 -o results
Beginning to generate features at Wed Jun 21 15:38:44 2023
>> Collected feature of X chromosome heterozygosity
Finish generate features of X chromosome heterozygosity at Wed Jun 21 15:38:48 2023
>> Collected feature of X mapping rate
Finish generate features of X mapping rate at Wed Jun 21 15:41:11 2023
>> Combine features into a single file
>> Running sample classification based on GMM model
Error in if (G[1] == 1) { : missing value where TRUE/FALSE needed
Calls: Mclust -> eval -> eval -> mclustBIC
Execution halted
Analysis complete for seGMM at Wed Jun 21 15:41:12 2023
Total time elapsed: 2.0m:28.53s
Solved: The file names contained "_", which was cut off at some point during "seGMM". Switching "_" to "-" solved the issue.
There appears to be an error in the clustering. It worked for lower sample sizes. Now I have 649 samples and I get this error: