Differentiation of maternal and fetal sources

[Gh-Genetics]

Error: Unable to open file ./mutai/cow/C3-1/C3-1.QC.vcf. Exiting.
Traceback (most recent call last):
File "/opt/souporcell/souporcell_pipeline.py", line 586, in
final_vcf = freebayes(args, bam, fasta)
File "/opt/souporcell/souporcell_pipeline.py", line 398, in freebayes
subprocess.check_call(["bedtools", "intersect", "-wa", "-a", args.common_variants, "-b", args.out_dir + "/depth_merged.bed"], stdout = vcf)
File "/opt/conda/envs/py36/lib/python3.6/subprocess.py", line 311, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bedtools', 'intersect', '-wa', '-a', './mutai/cow/C3-1/C3-1.QC.vcf', '-b', './output/depth_merged.bed']' returned non-zero exit status 1.