+ mkdir aih-tih-sc-3282fd-R1_A23YTGFLT4_1
+ all_qc -bam aih-tih-sc-3282fd-R1_A23YTGFLT4_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-3282fd-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_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-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_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-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai

0it [00:00, ?it/s]
157822it [00:00, 1577758.82it/s]
328040it [00:00, 1650868.10it/s]
501861it [00:00, 1690557.89it/s]
676226it [00:00, 1711485.56it/s]
850582it [00:00, 1722909.21it/s]
1024093it [00:00, 1727032.38it/s]
1197683it [00:00, 1729759.15it/s]
1372346it [00:00, 1735107.49it/s]
1546308it [00:00, 1736495.26it/s]
1719958it [00:01, 1735967.00it/s]
1893555it [00:01, 1728321.70it/s]
2067134it [00:01, 1730421.62it/s]
2240435it [00:01, 1731185.68it/s]
2417655it [00:01, 1743418.83it/s]
2592925it [00:01, 1746194.81it/s]
2767549it [00:01, 1741348.08it/s]
2941690it [00:01, 1737744.77it/s]
3118356it [00:01, 1746385.96it/s]
3293850it [00:01, 1748927.27it/s]
3468748it [00:02, 1729455.39it/s]
3644320it [00:02, 1737247.02it/s]
3818087it [00:02, 1736933.99it/s]
3994563it [00:02, 1745226.43it/s]
4169110it [00:02, 1744343.24it/s]
4343562it [00:02, 1739916.53it/s]
4518604it [00:02, 1742899.12it/s]
4692905it [00:02, 1701715.59it/s]
4863879it [00:02, 1703989.27it/s]
5039373it [00:02, 1719056.58it/s]
5212156it [00:03, 1721638.15it/s]
5384957it [00:03, 1723514.62it/s]
5559644it [00:03, 1730466.62it/s]
5732740it [00:03, 1725767.95it/s]
5905353it [00:03, 1718269.12it/s]
6077285it [00:03, 1718557.32it/s]
6249162it [00:03, 1713916.76it/s]
6420570it [00:03, 1707330.88it/s]
6592802it [00:03, 1711774.99it/s]
6764775it [00:03, 1714126.07it/s]
6936198it [00:04, 1705269.83it/s]
7110034it [00:04, 1715115.86it/s]
7282840it [00:04, 1718961.85it/s]
7456582it [00:04, 1724463.13it/s]
7629814it [00:04, 1726677.93it/s]
7802490it [00:04, 1726013.90it/s]
7976538it [00:04, 1730326.34it/s]
8150166it [00:04, 1732091.49it/s]
8323379it [00:04, 1731447.59it/s]
8499341it [00:04, 1739873.82it/s]
8674441it [00:05, 1743123.23it/s]
8850885it [00:05, 1749436.20it/s]
9026503it [00:05, 1751434.17it/s]
9201648it [00:05, 1741584.58it/s]
9378177it [00:05, 1748643.86it/s]
9553087it [00:05, 1748760.85it/s]
9728076it [00:05, 1749075.69it/s]
9902990it [00:05, 1741158.84it/s]
10078103it [00:05, 1744084.77it/s]
10253005it [00:05, 1745542.79it/s]
10427661it [00:06, 1745825.39it/s]
10602249it [00:06, 1745359.83it/s]
10776789it [00:06, 1740482.17it/s]
10951347it [00:06, 1741989.08it/s]
11126308it [00:06, 1744250.16it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai

11300737it [00:06, 1743081.08it/s]
11475048it [00:06, 1737205.39it/s]
11648774it [00:06, 1736985.72it/s]
11823283it [00:06, 1739355.66it/s]
11997325it [00:06, 1739653.79it/s]
12162132it [00:07, 1731730.97it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_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-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
+ merge_qc -folders aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md -output aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_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-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1_full_basic_stats.tsv