+ mkdir aih-tih-sc-cf89e7-R1_A23WJ53LT4_1
+ all_qc -bam aih-tih-sc-cf89e7-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-cf89e7-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-cf89e7-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-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-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-cf89e7-R1_A23WJ53LT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
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1596326it [00:01, 1526977.36it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
1772642it [00:01, 1598470.29it/s]
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3338536it [00:02, 1757157.92it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
3518399it [00:02, 1769455.76it/s]
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3874594it [00:02, 1529260.25it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
4033520it [00:02, 1401583.76it/s]
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5144811it [00:03, 1101116.68it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
5259725it [00:03, 1114761.34it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
5374222it [00:03, 1123462.28it/s]
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[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-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-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md.bai
+ merge_qc -folders aih-tih-sc-cf89e7-R1_A23WJ53LT4_1/aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.md -output aih-tih-sc-cf89e7-R1_A23WJ53LT4_1/aih-tih-sc-cf89e7-R1_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-cf89e7-R1_A23WJ53LT4_1/aih-tih-sc-cf89e7-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-cf89e7-R1_A23WJ53LT4_1/aih-tih-sc-cf89e7-R1_A23WJ53LT4_1_full_basic_stats.tsv