+ mkdir aih-tih-sc-24ecfe-R1_A23YTGFLT4_1
+ all_qc -bam aih-tih-sc-24ecfe-R1_A23YTGFLT4_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 aih-tih-sc-24ecfe-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_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: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai

0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai

97081it [00:00, 970697.52it/s]
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800946it [00:00, 1029560.61it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai

933667it [00:00, 1122293.74it/s]
1045932it [00:01, 1109641.64it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai

1156951it [00:01, 1097151.80it/s]
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1375576it [00:01, 1082110.40it/s]
1483818it [00:01, 1080573.96it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai

1591895it [00:01, 1076197.81it/s]
1699528it [00:01, 1075935.05it/s]
1807130it [00:01, 1073098.45it/s]
1876957it [00:01, 1049363.04it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_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: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bai
+ merge_qc -folders aih-tih-sc-24ecfe-R1_A23YTGFLT4_1/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md -output aih-tih-sc-24ecfe-R1_A23YTGFLT4_1/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-24ecfe-R1_A23YTGFLT4_1/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-24ecfe-R1_A23YTGFLT4_1/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1_full_basic_stats.tsv