+ mkdir aih-tih-sc-2482ef-R1_A23WJ53LT4_1
+ all_qc -bam aih-tih-sc-2482ef-R1_A23WJ53LT4_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-2482ef-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_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-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_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-2482ef-R1_A23WJ53LT4_1.md.bai

0it [00:00, ?it/s]
104002it [00:00, 1039649.18it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai

214128it [00:00, 1075837.85it/s]
324699it [00:00, 1089224.61it/s]
435627it [00:00, 1097057.43it/s]
547508it [00:00, 1104866.36it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai

659130it [00:00, 1108699.47it/s]
770808it [00:00, 1111313.53it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai

882971it [00:00, 1114566.54it/s]
996143it [00:00, 1119780.32it/s]
1109277it [00:01, 1123312.46it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai

1222458it [00:01, 1125884.40it/s]
1357801it [00:01, 1195068.11it/s]
1492744it [00:01, 1241793.57it/s]
1528344it [00:01, 1152749.23it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_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-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bai
+ merge_qc -folders aih-tih-sc-2482ef-R1_A23WJ53LT4_1/aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md -output aih-tih-sc-2482ef-R1_A23WJ53LT4_1/aih-tih-sc-2482ef-R1_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-2482ef-R1_A23WJ53LT4_1/aih-tih-sc-2482ef-R1_A23WJ53LT4_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-2482ef-R1_A23WJ53LT4_1/aih-tih-sc-2482ef-R1_A23WJ53LT4_1_full_basic_stats.tsv