+ mkdir BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1
+ all_qc -bam BreastNP_FFPE_L04_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 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_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: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_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: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai

0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai

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209370it [00:00, 703511.74it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai

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1071532it [00:01, 721045.08it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai

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1577828it [00:02, 715150.00it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai

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[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_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: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bai
+ merge_qc -folders BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md -output BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv
+ head -n1 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_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 BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv