+ mkdir tih_rna_sample_00584_B23MVV7LT4_1
+ all_qc -bam tih_rna_sample_00584_B23MVV7LT4_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 tih_rna_sample_00584_B23MVV7LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_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: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai

0it [00:00, ?it/s]
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528974it [00:00, 1781853.67it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai

712860it [00:00, 1804323.36it/s]
894496it [00:00, 1808630.12it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai

1075360it [00:00, 1808181.17it/s]
1257606it [00:00, 1812704.83it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai

1441369it [00:00, 1820608.51it/s]
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1900456it [00:01, 1808099.18it/s]
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_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: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00584_B23MVV7LT4_1.md.bai
+ merge_qc -folders tih_rna_sample_00584_B23MVV7LT4_1/tih_rna_sample_00584_B23MVV7LT4_1.md -output tih_rna_sample_00584_B23MVV7LT4_1/tih_rna_sample_00584_B23MVV7LT4_1_full_basic_stats.tsv
+ head -n1 tih_rna_sample_00584_B23MVV7LT4_1/tih_rna_sample_00584_B23MVV7LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00584_B23MVV7LT4_1/tih_rna_sample_00584_B23MVV7LT4_1_full_basic_stats.tsv