+ mkdir aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1
+ all_qc -bam aih-tih-sc-2e5fe9-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-2e5fe9-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-2e5fe9-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-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-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-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
0it [00:00, ?it/s]
54169it [00:00, 541649.19it/s]
111555it [00:00, 560576.80it/s]
168489it [00:00, 564555.01it/s]
227091it [00:00, 573013.87it/s]
284781it [00:00, 574335.87it/s]
342403it [00:00, 574964.94it/s]
400246it [00:00, 576083.00it/s]
457855it [00:00, 575510.16it/s]
515840it [00:00, 576855.28it/s]
573890it [00:01, 577931.59it/s]
632093it [00:01, 579166.55it/s]
690300it [00:01, 580037.50it/s]
748515it [00:01, 580659.86it/s]
806582it [00:01, 580088.79it/s]
865697it [00:01, 583405.75it/s]
924971it [00:01, 586202.52it/s]
983592it [00:01, 567384.73it/s]
1050803it [00:01, 598110.34it/s]
1143424it [00:01, 695042.95it/s]
1235625it [00:02, 762391.84it/s]
1330057it [00:02, 816549.85it/s]
1423330it [00:02, 851204.04it/s]
1516631it [00:02, 875603.55it/s]
1610291it [00:02, 893838.63it/s]
1699776it [00:02, 892697.56it/s]
1792270it [00:02, 902170.02it/s]
1882539it [00:02, 882848.42it/s]
1970950it [00:02, 869708.49it/s]
2062387it [00:02, 882791.96it/s]
2155575it [00:03, 897272.02it/s]
2250436it [00:03, 912485.83it/s]
2341772it [00:03, 900480.18it/s]
2438426it [00:03, 919985.40it/s]
2535304it [00:03, 934453.53it/s]
2630345it [00:03, 939160.79it/s]
2724788it [00:03, 940716.87it/s]
2819622it [00:03, 942982.94it/s]
2913951it [00:03, 846022.94it/s]
3000438it [00:03, 790310.91it/s]
3081278it [00:04, 715209.07it/s]
3154994it [00:04, 679600.87it/s]
3224482it [00:04, 653538.42it/s]
3290811it [00:04, 633112.94it/s]
3354703it [00:04, 617531.60it/s]
3416772it [00:04, 606278.02it/s]
3477552it [00:04, 599527.46it/s]
3537567it [00:04, 596042.90it/s]
3597194it [00:05, 592134.99it/s]
3656748it [00:05, 593101.11it/s]
3716331it [00:05, 593881.36it/s]
3775725it [00:05, 590726.58it/s]
3834799it [00:05, 588895.62it/s]
3894770it [00:05, 592077.45it/s]
3953982it [00:05, 590386.15it/s]
4014114it [00:05, 593620.74it/s]
4073481it [00:05, 592871.67it/s]
4132772it [00:05, 590483.04it/s]
4191824it [00:06, 590212.90it/s]
4250992it [00:06, 590576.97it/s]
4310052it [00:06, 589238.67it/s]
4374723it [00:06, 606396.87it/s]
4463057it [00:06, 689223.99it/s]
4550861it [00:06, 745736.58it/s]
4640510it [00:06, 790826.44it/s]
4730460it [00:06, 823363.82it/s]
4812820it [00:06, 797068.20it/s]
4892949it [00:06, 798290.55it/s]
4972920it [00:07, 797229.43it/s]
5052792it [00:07, 797655.90it/s]
5136779it [00:07, 810139.19it/s]
5217853it [00:07, 805303.79it/s]
5305873it [00:07, 827466.05it/s]
5394818it [00:07, 845929.29it/s]
5483902it [00:07, 859317.65it/s]
5574203it [00:07, 872368.65it/s]
5664656it [00:07, 881980.42it/s]
5753785it [00:07, 884753.43it/s]
5844838it [00:08, 892456.50it/s]
5934574it [00:08, 893835.30it/s]
6023967it [00:08, 888181.74it/s]
6112800it [00:08, 879754.16it/s]
6200800it [00:08, 867337.33it/s]
6288905it [00:08, 871278.37it/s]
6378222it [00:08, 877751.95it/s]
6466032it [00:08, 868053.40it/s]
6554919it [00:08, 874102.85it/s]
6642367it [00:08, 837770.58it/s]
6726464it [00:09, 746242.49it/s]
6802993it [00:09, 698979.88it/s]
6874516it [00:09, 668530.89it/s]
6942502it [00:09, 648502.61it/s]
7008066it [00:09, 633129.47it/s]
7071803it [00:09, 621615.00it/s]
7134201it [00:09, 613718.46it/s]
7195695it [00:09, 609246.08it/s]
7256681it [00:10, 604182.68it/s]
7317124it [00:10, 600354.59it/s]
7377165it [00:10, 596874.58it/s]
7436849it [00:10, 596632.04it/s]
7496685it [00:10, 597068.86it/s]
7556391it [00:10, 596061.68it/s]
7615995it [00:10, 595905.48it/s]
7676546it [00:10, 598748.51it/s]
7736422it [00:10, 598681.02it/s]
7796291it [00:10, 595614.40it/s]
7856362it [00:11, 597121.30it/s]
7916078it [00:11, 596518.93it/s]
7975732it [00:11, 596417.90it/s]
8035376it [00:11, 595749.13it/s]
8094952it [00:11, 595181.17it/s]
8154471it [00:11, 594549.49it/s]
8213927it [00:11, 592874.52it/s]
8273216it [00:11, 591306.50it/s]
8332561it [00:11, 591934.59it/s]
8391756it [00:11, 591593.49it/s]
8450916it [00:12, 589757.09it/s]
8509894it [00:12, 589207.11it/s]
8568816it [00:12, 587189.63it/s]
8628147it [00:12, 589006.13it/s]
8687050it [00:12, 587416.84it/s]
8746437it [00:12, 589333.33it/s]
8805373it [00:12, 588995.39it/s]
8864274it [00:12, 588529.23it/s]
8923245it [00:12, 588823.98it/s]
8982291it [00:12, 589258.58it/s]
9041709it [00:13, 590720.24it/s]
9101143it [00:13, 591791.41it/s]
9160715it [00:13, 592951.60it/s]
9220839it [00:13, 595423.07it/s]
9280382it [00:13, 585042.03it/s]
9338927it [00:13, 568338.28it/s]
9396959it [00:13, 571730.68it/s]
9478140it [00:13, 642260.56it/s]
9562330it [00:13, 701271.01it/s]
9652814it [00:13, 761705.63it/s]
9738666it [00:14, 790528.59it/s]
9825315it [00:14, 813119.40it/s]
9906764it [00:14, 801290.98it/s]
9988090it [00:14, 804818.42it/s]
10075344it [00:14, 824930.36it/s]
10157942it [00:14, 825225.85it/s]
10243419it [00:14, 834033.46it/s]
10326869it [00:14, 833152.71it/s]
10410217it [00:14, 824644.27it/s]
10495945it [00:14, 834328.23it/s]
10579416it [00:15, 819553.79it/s]
10661448it [00:15, 815344.77it/s]
10749132it [00:15, 833484.79it/s]
10834769it [00:15, 840259.71it/s]
10918849it [00:15, 835045.44it/s]
11005113it [00:15, 843224.72it/s]
11090656it [00:15, 846842.80it/s]
11176680it [00:15, 850803.60it/s]
11265789it [00:15, 862813.10it/s]
11353317it [00:15, 866526.84it/s]
11441110it [00:16, 869926.53it/s]
11528114it [00:16, 861902.26it/s]
11615370it [00:16, 865060.92it/s]
11701895it [00:16, 862921.27it/s]
11788201it [00:16, 827564.32it/s]
11871261it [00:16, 739431.31it/s]
11947014it [00:16, 689564.62it/s]
12017604it [00:16, 658374.90it/s]
12084595it [00:16, 634814.11it/s]
12148825it [00:17, 620037.43it/s]
12211272it [00:17, 609930.47it/s]
12272513it [00:17, 601812.15it/s]
12332825it [00:17, 597036.02it/s]
12392594it [00:17, 594455.72it/s]
12452073it [00:17, 590283.06it/s]
12511114it [00:17, 589916.01it/s]
12570113it [00:17, 589369.50it/s]
12629054it [00:17, 588782.52it/s]
12687934it [00:18, 588752.98it/s]
12746811it [00:18, 584787.99it/s]
12805783it [00:18, 586238.05it/s]
12864411it [00:18, 586024.55it/s]
12923435it [00:18, 587271.28it/s]
12982165it [00:18, 583835.38it/s]
13040556it [00:18, 583845.75it/s]
13098945it [00:18, 583702.51it/s]
13157613it [00:18, 584581.39it/s]
13216074it [00:18, 584294.58it/s]
13274613it [00:19, 584610.98it/s]
13333076it [00:19, 583390.69it/s]
13391417it [00:19, 582833.20it/s]
13450252it [00:19, 584470.17it/s]
13498098it [00:19, 695942.99it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-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-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bai
+ merge_qc -folders aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md -output aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1/aih-tih-sc-2e5fe9-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-2e5fe9-R1_A23YTGFLT4_1/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1_full_basic_stats.tsv