+ mkdir BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1
+ all_qc -bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_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 BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
/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
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai

0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai

98774it [00:00, 987620.85it/s]
197537it [00:00, 851988.15it/s]
283925it [00:00, 827832.35it/s]
372932it [00:00, 850642.10it/s]
458505it [00:00, 836676.31it/s]
542480it [00:00, 825590.63it/s]
625226it [00:00, 801459.04it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai

709919it [00:00, 815220.62it/s]
794610it [00:00, 824765.00it/s]
877251it [00:01, 824378.10it/s]
959802it [00:01, 824471.10it/s]
1042328it [00:01, 815700.14it/s]
1125149it [00:01, 819400.37it/s]
1207245it [00:01, 819833.70it/s]
1289266it [00:01, 815759.33it/s]
1371877it [00:01, 818792.62it/s]
1457746it [00:01, 830676.79it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai

1542452it [00:01, 835493.07it/s]
1626020it [00:01, 832186.80it/s]
1709254it [00:02, 816651.01it/s]
1790988it [00:02, 816542.02it/s]
1874874it [00:02, 823129.46it/s][W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai

1958848it [00:02, 828037.92it/s]
2042339it [00:02, 830062.48it/s]
2125665it [00:02, 830905.60it/s]
2208773it [00:02, 821503.54it/s]
2290958it [00:02, 814106.57it/s]
2376345it [00:02, 825846.40it/s]
2463880it [00:02, 840529.11it/s]
2530074it [00:03, 829366.11it/s]
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bai
+ merge_qc -folders BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md -output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv
+ head -n1 BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv