+ mkdir aih-tih-sc-9fb608-R1_A23WJ53LT4_1
+ all_qc -bam aih-tih-sc-9fb608-R1_A23WJ53LT4_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-9fb608-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_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-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_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-9fb608-R1_A23WJ53LT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
150069it [00:00, 1500405.25it/s]
312933it [00:00, 1575801.51it/s]
479166it [00:00, 1615149.09it/s]
647736it [00:00, 1642868.42it/s]
819782it [00:00, 1670828.77it/s]
986866it [00:00, 1670685.52it/s]
1158123it [00:00, 1684361.78it/s]
1328703it [00:00, 1691173.80it/s]
1500957it [00:00, 1700965.30it/s]
1672849it [00:01, 1706493.45it/s]
1846029it [00:01, 1714226.25it/s]
2017452it [00:01, 1711515.62it/s]
2188605it [00:01, 1700022.35it/s]
2358625it [00:01, 1696718.67it/s]
2532551it [00:01, 1709463.36it/s]
2703513it [00:01, 1708409.00it/s]
2877258it [00:01, 1717067.97it/s]
3051857it [00:01, 1725590.25it/s]
3224425it [00:01, 1724151.97it/s]
3396847it [00:02, 1702136.72it/s]
3567126it [00:02, 1695852.53it/s]
3740172it [00:02, 1706109.94it/s]
3910825it [00:02, 1703246.39it/s]
4083149it [00:02, 1709184.31it/s]
4257785it [00:02, 1720107.81it/s]
4429854it [00:02, 1720264.04it/s]
4602949it [00:02, 1723440.28it/s]
4778735it [00:02, 1733656.20it/s]
4953722it [00:02, 1738453.55it/s]
5127575it [00:03, 1731833.96it/s]
5300769it [00:03, 1725407.94it/s]
5473321it [00:03, 1692691.28it/s]
5642722it [00:03, 1680071.79it/s]
5816117it [00:03, 1695822.86it/s]
5988409it [00:03, 1703828.74it/s]
6160997it [00:03, 1710366.41it/s]
6333185it [00:03, 1713780.80it/s]
6504606it [00:03, 1711175.78it/s]
6676493it [00:03, 1713456.85it/s]
6847861it [00:04, 1710084.66it/s]
7018886it [00:04, 1706162.51it/s]
7190922it [00:04, 1710390.54it/s]
7364081it [00:04, 1716719.49it/s]
7537501it [00:04, 1721941.47it/s]
7710677it [00:04, 1724868.64it/s]
7883170it [00:04, 1717062.13it/s]
8056760it [00:04, 1722665.14it/s]
8229066it [00:04, 1722615.43it/s]
8402054it [00:04, 1724776.22it/s]
8576131it [00:05, 1729555.83it/s]
8749091it [00:05, 1724215.07it/s]
8922636it [00:05, 1727561.65it/s]
9095398it [00:05, 1718587.41it/s]
9271182it [00:05, 1730290.67it/s]
9444461it [00:05, 1731018.57it/s]
9617574it [00:05, 1729958.83it/s]
9790578it [00:05, 1727251.91it/s]
9963309it [00:05, 1719877.66it/s]
10135989it [00:05, 1721931.31it/s]
10308418it [00:06, 1722624.72it/s]
10481673it [00:06, 1725582.14it/s]
10654236it [00:06, 1701833.65it/s]
10824493it [00:06, 1701146.36it/s]
10994754it [00:06, 1701566.73it/s]
11166177it [00:06, 1705331.54it/s]
11339139it [00:06, 1712575.21it/s]
11510419it [00:06, 1712385.23it/s]
11683874it [00:06, 1718940.58it/s]
11858471it [00:06, 1727026.93it/s]
12034687it [00:07, 1737545.32it/s]
12208450it [00:07, 1736089.63it/s]
12382956it [00:07, 1738765.84it/s]
12556837it [00:07, 1732139.17it/s]
12730060it [00:07, 1725896.28it/s]
12902659it [00:07, 1721175.94it/s]
13077013it [00:07, 1727837.92it/s]
13251088it [00:07, 1731686.57it/s]
13424720it [00:07, 1733061.11it/s]
13598200it [00:07, 1733569.94it/s]
13771561it [00:08, 1731715.77it/s]
13945001it [00:08, 1732509.06it/s]
14118255it [00:08, 1720471.95it/s]
14290981it [00:08, 1722481.35it/s]
14463244it [00:08, 1721380.88it/s]
14635393it [00:08, 1720821.45it/s]
14809203it [00:08, 1725972.70it/s]
14981807it [00:08, 1721883.48it/s]
15156850it [00:08, 1730406.94it/s]
15329898it [00:08, 1725962.16it/s]
15504467it [00:09, 1731848.24it/s]
15678976it [00:09, 1735798.60it/s]
15853282it [00:09, 1737959.14it/s]
16027082it [00:09, 1732437.94it/s]
16202212it [00:09, 1738068.82it/s]
16376025it [00:09, 1729690.22it/s]
16549006it [00:09, 1718336.05it/s]
16685428it [00:09, 1715021.21it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_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-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai
+ merge_qc -folders aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md -output aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_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-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1_full_basic_stats.tsv