+ mkdir 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1
+ all_qc -bam 1173_CI9_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_CI9_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_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: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai

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[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_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: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
+ merge_qc -folders 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
+ head -n1 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_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_CI9_T1_RNA_SLD_01_A23T55JLT4_1/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv