+ mkdir 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2
+ all_qc -bam 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.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 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.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: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai

0it [00:00, ?it/s]
100294it [00:00, 1002768.82it/s]
210249it [00:00, 1059597.45it/s][W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai

320672it [00:00, 1079896.34it/s]
432030it [00:00, 1093115.19it/s]
541986it [00:00, 1095379.10it/s][W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai

622437it [00:00, 1087160.57it/s]
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.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: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
+ merge_qc -folders 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md -output 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv
+ head -n1 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv