+ mkdir 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1
+ all_qc -bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -beds Twist_rna_exome_AND_fusion_hg38.bed -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz -contamination_bed dbsnp_hg38_contam_sites.bed -output_folder 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20
[mpileup] 1 samples in 1 input files
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources

0it [00:00, ?it/s]
98536it [00:00, 985236.44it/s]
201637it [00:00, 1012094.53it/s]
302847it [00:00, 996046.62it/s] 
402482it [00:00, 991287.79it/s]
504724it [00:00, 1002377.23it/s]
608225it [00:00, 1013374.42it/s]
630734it [00:00, 1005909.29it/s]
+ merge_qc -folders 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
+ head -n1 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv