+ mkdir 659_bjQ-T1-TRNA-1_B23MHV2LT4_1
+ all_qc -bam 659_bjQ-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_bjQ-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_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai

0it [00:00, ?it/s]
144721it [00:00, 1447121.67it/s]
299546it [00:00, 1506561.79it/s]
458101it [00:00, 1542583.71it/s]
616262it [00:00, 1557951.30it/s]
778132it [00:00, 1579676.79it/s]
940792it [00:00, 1595590.82it/s]
1101506it [00:00, 1599329.31it/s]
1263036it [00:00, 1604375.98it/s]
1423475it [00:00, 1604350.95it/s]
1585868it [00:01, 1610364.71it/s]
1753478it [00:01, 1630452.76it/s]
1916882it [00:01, 1631426.14it/s]
2080025it [00:01, 1620320.40it/s]
2242075it [00:01, 1607791.09it/s]
2406984it [00:01, 1619954.23it/s]
2569010it [00:01, 1616474.76it/s]
2732231it [00:01, 1621144.16it/s]
2894363it [00:01, 1608593.85it/s]
3055252it [00:01, 1603404.15it/s]
3215613it [00:02, 1592842.18it/s]
3378346it [00:02, 1603060.38it/s]
3541504it [00:02, 1611531.45it/s]
3702876it [00:02, 1612157.75it/s]
3864110it [00:02, 1611175.63it/s]
4030819it [00:02, 1627876.11it/s]
4193620it [00:02, 1627298.68it/s]
4358736it [00:02, 1634418.78it/s]
4523122it [00:02, 1637220.21it/s]
4686850it [00:02, 1556560.12it/s]
4843337it [00:03, 1506395.87it/s]
4995043it [00:03, 1509400.79it/s]
5146555it [00:03, 1510623.69it/s]
5298022it [00:03, 1494956.83it/s]
5451303it [00:03, 1505987.77it/s]
5615244it [00:03, 1545266.32it/s]
5778847it [00:03, 1572113.03it/s]
5936254it [00:03, 1541359.54it/s]
6090639it [00:03, 1496128.34it/s]
6240642it [00:03, 1484940.44it/s]
6401908it [00:04, 1522060.49it/s]
6562750it [00:04, 1547380.91it/s]
6723532it [00:04, 1565134.86it/s]
6885564it [00:04, 1581401.18it/s]
7049770it [00:04, 1599424.84it/s]
7215377it [00:04, 1616299.34it/s]
7379537it [00:04, 1623670.59it/s]
7541977it [00:04, 1619535.19it/s]
7703983it [00:04, 1605827.76it/s]
7864625it [00:04, 1602688.27it/s]
8024934it [00:05, 1590651.59it/s]
8184711it [00:05, 1592739.06it/s]
8344016it [00:05, 1577004.67it/s]
8506544it [00:05, 1591276.59it/s]
8670024it [00:05, 1604185.81it/s]
8834286it [00:05, 1615616.01it/s]
8997901it [00:05, 1621695.11it/s]
9166308it [00:05, 1640319.23it/s]
9330367it [00:05, 1635910.09it/s]
9493979it [00:05, 1623840.22it/s]
9658707it [00:06, 1630795.04it/s]
9824121it [00:06, 1637733.73it/s]
9987917it [00:06, 1635650.26it/s]
10152837it [00:06, 1639674.37it/s]
10318135it [00:06, 1643630.78it/s]
10482508it [00:06, 1637174.51it/s]
10646237it [00:06, 1632971.49it/s]
10813044it [00:06, 1643423.72it/s]
10977398it [00:06, 1640468.42it/s]
11142704it [00:06, 1644207.19it/s]
11308588it [00:07, 1648481.87it/s]
11473443it [00:07, 1642870.16it/s]
11638260it [00:07, 1644429.00it/s]
11802709it [00:07, 1642836.18it/s]
11966997it [00:07, 1640535.70it/s]
12131054it [00:07, 1581789.03it/s]
12289675it [00:07, 1492744.99it/s]
12451641it [00:07, 1528521.76it/s]
12614723it [00:07, 1557886.61it/s]
12776892it [00:08, 1576429.18it/s]
12942528it [00:08, 1599871.95it/s]
13103029it [00:08, 1583786.91it/s]
13265120it [00:08, 1594527.93it/s]
13428163it [00:08, 1605134.10it/s]
13596460it [00:08, 1628190.46it/s]
13762050it [00:08, 1636419.18it/s]
13925816it [00:08, 1632254.06it/s]
14090426it [00:08, 1636261.39it/s]
14183067it [00:08, 1597403.44it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md.bai
+ merge_qc -folders 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
+ head -n1 659_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-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_bjQ-T1-TRNA-1_B23MHV2LT4_1/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv