+ mkdir 659_bMa-T1-TRNA-1_B23MHV2LT4_1
+ all_qc -bam 659_bMa-T1-TRNA-1_B23MHV2LT4_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 659_bMa-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_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: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
0it [00:00, ?it/s]
164509it [00:00, 1644969.99it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
341159it [00:00, 1716418.53it/s]
522613it [00:00, 1761195.52it/s]
705551it [00:00, 1788092.08it/s]
886659it [00:00, 1796289.45it/s]
1067079it [00:00, 1798957.62it/s]
1248532it [00:00, 1804032.07it/s]
1428936it [00:00, 1794921.23it/s]
1608862it [00:00, 1796254.70it/s]
1791060it [00:01, 1804157.99it/s]
1973069it [00:01, 1808947.21it/s]
2156321it [00:01, 1816093.05it/s]
2337935it [00:01, 1813668.15it/s]
2521287it [00:01, 1819506.57it/s]
2703648it [00:01, 1820720.38it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
2885723it [00:01, 1816163.89it/s]
3067344it [00:01, 1792212.93it/s]
3247479it [00:01, 1794912.64it/s]
3429175it [00:01, 1801467.67it/s]
3609363it [00:02, 1786687.42it/s]
3790591it [00:02, 1794278.81it/s]
3971476it [00:02, 1798606.42it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
4154386it [00:02, 1807696.37it/s]
4336616it [00:02, 1812048.80it/s]
4517841it [00:02, 1810129.11it/s]
4700830it [00:02, 1816028.72it/s]
4882445it [00:02, 1809922.47it/s]
5063666it [00:02, 1810591.36it/s]
5244734it [00:02, 1805145.83it/s]
5426723it [00:03, 1809538.44it/s]
5609185it [00:03, 1813905.02it/s]
5791387it [00:03, 1816321.04it/s]
5974267it [00:03, 1819928.84it/s]
6156264it [00:03, 1812266.65it/s]
6337501it [00:03, 1804229.90it/s]
6517936it [00:03, 1802969.87it/s]
6698241it [00:03, 1792946.96it/s]
6877550it [00:03, 1790803.75it/s]
7056640it [00:03, 1788344.22it/s]
7235481it [00:04, 1778602.87it/s]
7414664it [00:04, 1782514.52it/s]
7596055it [00:04, 1791860.80it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
7777019it [00:04, 1797111.67it/s]
7961078it [00:04, 1810104.10it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
8113870it [00:04, 1801320.16it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_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: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai
+ merge_qc -folders 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
+ head -n1 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv