[2024-Apr-03 23:50:54]Parsing and checking arguments
[2024-Apr-03 23:50:54]A matched-normal sample has not been provided and the presence of the provided heterozygous germline SNPs will not be correspondigly assessed.
[2024-Apr-03 23:50:54]Arguments:
	normal : None
	bcftools : bcftools
	J : 56
	cellprefix : CB:Z:
	seqerr : 0.001
	cellsuffix : 
	rundir : /net/mulan/home/kalinsba/DATA/slideDNA_scWGS/apply_chisel/outputs/nonnormal/human_colon_cancer_3_scwgs_200227_01
	samtools : samtools
	list : /net/mulan/home/kalinsba/DATA/slideDNA_scWGS/apply_chisel/outputs/nonnormal/human_colon_cancer_3_scwgs_200227_01/rdr/total.tsv
	tumor : /net/mulan/home/kalinsba/DATA/slideDNA_scWGS/Downloaded_BAMs/human_colon_cancer_3_scwgs_200227_01.bam
	phased : /net/mulan/home/kalinsba/DATA/slideDNA_scWGS/eagle2/output/chromosome_wise/human_colon_cancer_3_scwgs_200227_01/concatinated/phased_het_chr_prefix_removed.vcf.gz
	ref : /net/mulan/home/kalinsba/DATA/slideDNA_scWGS/apply_chisel/inputs/ref_genome/refdata-GRCh37-1.0.0/fasta/genome.fa
	gamma : 0.01
[2024-Apr-03 23:50:54]Extracting chromosomes
Traceback (most recent call last):
  File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/site-packages/chisel/BAFEstimator.py", line 326, in <module>
    main()
  File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/site-packages/chisel/BAFEstimator.py", line 96, in main
    phased = read_phase(args['phased'])
  File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/site-packages/chisel/BAFEstimator.py", line 148, in read_phase
    if len(l) > 1 and p[0][0] != '#':
IndexError: list index out of range