+ mkdir 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1
+ all_qc -bam 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_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 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_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: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
154645it [00:00, 1546374.05it/s]
322047it [00:00, 1621418.36it/s]
492863it [00:00, 1660993.63it/s]
666662it [00:00, 1691365.29it/s]
841090it [00:00, 1710424.75it/s]
1015485it [00:00, 1721798.51it/s]
1189436it [00:00, 1727566.30it/s]
1362907it [00:00, 1729818.66it/s]
1537403it [00:00, 1734529.19it/s]
1712196it [00:01, 1738647.50it/s]
1886061it [00:01, 1725616.86it/s]
2058645it [00:01, 1725419.73it/s]
2238121it [00:01, 1746325.30it/s]
2415772it [00:01, 1755396.27it/s]
2591327it [00:01, 1747501.83it/s]
2766095it [00:01, 1741872.27it/s]
2940818it [00:01, 1743450.27it/s]
3116888it [00:01, 1748570.80it/s]
3291755it [00:01, 1745882.91it/s]
3466351it [00:02, 1725680.59it/s]
3641379it [00:02, 1732951.67it/s]
3814719it [00:02, 1719544.67it/s]
3986719it [00:02, 1717200.38it/s]
4158470it [00:02, 1691297.96it/s]
4327931it [00:02, 1692237.70it/s]
4501581it [00:02, 1705328.94it/s]
4673701it [00:02, 1710016.97it/s]
4846901it [00:02, 1716472.22it/s]
5022720it [00:02, 1728805.72it/s]
5199264it [00:03, 1739731.30it/s]
5377937it [00:03, 1753765.18it/s]
5553334it [00:03, 1750357.86it/s]
5728385it [00:03, 1747799.88it/s]
5903176it [00:03, 1737041.17it/s]
6076901it [00:03, 1730128.62it/s]
6252971it [00:03, 1739206.32it/s]
6427072it [00:03, 1739714.24it/s]
6601057it [00:03, 1737787.26it/s]
6774987it [00:03, 1738212.83it/s]
6948815it [00:04, 1722373.19it/s]
7122644it [00:04, 1727085.94it/s]
7297240it [00:04, 1732690.87it/s]
7470660it [00:04, 1733012.68it/s]
7645037it [00:04, 1736210.19it/s]
7821404it [00:04, 1744409.83it/s]
7997003it [00:04, 1747857.04it/s]
8171797it [00:04, 1745178.88it/s]
8347601it [00:04, 1748899.75it/s]
8522837it [00:04, 1749916.98it/s]
8698456it [00:05, 1751778.88it/s]
8874817it [00:05, 1755303.84it/s]
9050962it [00:05, 1757123.47it/s]
9227162it [00:05, 1758566.32it/s]
9403020it [00:05, 1739765.45it/s]
9578799it [00:05, 1745113.22it/s][W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
9754820it [00:05, 1749598.41it/s]
9929808it [00:05, 1744048.60it/s]
10104235it [00:05, 1712754.05it/s]
10279027it [00:05, 1723114.17it/s]
10456245it [00:06, 1737647.01it/s]
10632168it [00:06, 1744031.30it/s]
10807823it [00:06, 1747615.99it/s]
10983774it [00:06, 1751151.76it/s]
11159656it [00:06, 1753427.53it/s]
11335025it [00:06, 1746411.81it/s]
11509923it [00:06, 1747162.10it/s]
11684656it [00:06, 1737640.15it/s]
11859475it [00:06, 1740768.33it/s]
12034747it [00:06, 1744318.32it/s]
12211740it [00:07, 1751962.41it/s]
12390798it [00:07, 1763508.07it/s]
12567198it [00:07, 1763517.39it/s]
12743557it [00:07, 1755592.03it/s]
12923196it [00:07, 1767665.77it/s]
13101564it [00:07, 1772434.42it/s]
13278819it [00:07, 1771131.87it/s]
13455940it [00:07, 1767850.42it/s]
13632732it [00:07, 1756631.18it/s][W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
13808413it [00:07, 1750137.05it/s]
13983728it [00:08, 1751018.92it/s]
14159656it [00:08, 1753465.55it/s]
14335057it [00:08, 1753612.57it/s]
14511247it [00:08, 1756074.45it/s]
14686860it [00:08, 1746795.72it/s]
14861553it [00:08, 1744034.67it/s]
15039149it [00:08, 1753552.85it/s]
15217006it [00:08, 1761015.62it/s]
15394929it [00:08, 1766451.74it/s]
15571583it [00:08, 1764641.35it/s]
15750312it [00:09, 1771406.27it/s]
15927458it [00:09, 1767670.12it/s]
16104231it [00:09, 1760256.64it/s]
16280266it [00:09, 1760234.89it/s]
16288669it [00:09, 1740887.15it/s]
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_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: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
+ merge_qc -folders 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
+ head -n1 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv