+ mkdir 659_buD-T1-TRNA-1_B23WHTKLT4_1
+ all_qc -bam 659_buD-T1-TRNA-1_B23WHTKLT4_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_buD-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_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_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
0it [00:00, ?it/s]
147741it [00:00, 1477312.79it/s]
312328it [00:00, 1576418.07it/s]
480741it [00:00, 1625567.23it/s]
651199it [00:00, 1656733.76it/s]
822988it [00:00, 1678696.15it/s]
996494it [00:00, 1697841.51it/s]
1169853it [00:00, 1709421.97it/s]
1342016it [00:00, 1713196.84it/s]
1513336it [00:00, 1710322.75it/s]
1687625it [00:01, 1720341.08it/s]
1860415it [00:01, 1722556.32it/s]
2032673it [00:01, 1700076.31it/s]
2206981it [00:01, 1712956.07it/s]
2379175it [00:01, 1715632.29it/s]
2553357it [00:01, 1723467.22it/s]
2726906it [00:01, 1727052.39it/s]
2899636it [00:01, 1721306.14it/s]
3071787it [00:01, 1716202.16it/s]
3243423it [00:01, 1693097.96it/s]
3412804it [00:02, 1645631.92it/s]
3577657it [00:02, 1510935.79it/s]
3745166it [00:02, 1556309.43it/s]
3914101it [00:02, 1593965.50it/s]
4085720it [00:02, 1629123.28it/s]
4256332it [00:02, 1651539.14it/s]
4429116it [00:02, 1673957.32it/s]
4601373it [00:02, 1688320.34it/s]
4774251it [00:02, 1700325.00it/s]
4945802it [00:02, 1704795.94it/s]
5116540it [00:03, 1645426.23it/s]
5281691it [00:03, 1599099.77it/s]
5453998it [00:03, 1634763.42it/s]
5624676it [00:03, 1655721.58it/s]
5796235it [00:03, 1673288.82it/s]
5967036it [00:03, 1683529.85it/s]
6136842it [00:03, 1687735.69it/s]
6305807it [00:03, 1682793.42it/s]
6476681it [00:03, 1690496.19it/s]
6647735it [00:03, 1696381.37it/s]
6823164it [00:04, 1713669.66it/s]
6994589it [00:04, 1609683.16it/s]
7156870it [00:04, 1551591.82it/s]
7326340it [00:04, 1591985.95it/s]
7495194it [00:04, 1619727.14it/s]
7664670it [00:04, 1641555.97it/s]
7838776it [00:04, 1670756.15it/s]
8009963it [00:04, 1682889.87it/s]
8182438it [00:04, 1695303.66it/s]
8355344it [00:05, 1705342.65it/s]
8528970it [00:05, 1714553.75it/s]
8703639it [00:05, 1724144.46it/s]
8876163it [00:05, 1718300.28it/s][W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
9049605it [00:05, 1723036.25it/s]
9221967it [00:05, 1718339.42it/s]
9393844it [00:05, 1696367.62it/s]
9444184it [00:05, 1671768.07it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_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_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_B23WHTKLT4_1.md.bai
+ merge_qc -folders 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1.md -output 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv
+ head -n1 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_buD-T1-TRNA-1_B23WHTKLT4_1/659_buD-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv