+ mkdir 659_1q-T1-TRNA-1_B23MHV2LT4_1
+ all_qc -bam 659_1q-T1-TRNA-1_B23MHV2LT4_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_1q-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_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_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai

0it [00:00, ?it/s]
93615it [00:00, 936057.16it/s]
201946it [00:00, 1022392.49it/s]
304531it [00:00, 1023940.23it/s]
422831it [00:00, 1086700.39it/s]
536864it [00:00, 1106008.71it/s]
647466it [00:00, 1101493.41it/s]
757943it [00:00, 1102532.80it/s]
869879it [00:00, 1107857.94it/s]
980668it [00:00, 1107721.52it/s]
1091443it [00:01, 1093345.05it/s]
1200819it [00:01, 1080528.54it/s]
1316811it [00:01, 1104288.97it/s]
1427311it [00:01, 1103898.13it/s]
1539527it [00:01, 1109347.80it/s]
1653640it [00:01, 1118848.04it/s]
1765557it [00:01, 1110001.05it/s]
1876593it [00:01, 1086547.25it/s]
1991182it [00:01, 1103987.89it/s]
2103905it [00:01, 1110844.25it/s]
2216933it [00:02, 1116563.88it/s]
2333300it [00:02, 1130578.25it/s]
2447918it [00:02, 1135187.79it/s]
2561526it [00:02, 1135437.08it/s]
2675101it [00:02, 1083284.79it/s]
2783947it [00:02, 1068284.71it/s]
2891140it [00:02, 1059098.19it/s]
2998163it [00:02, 1062313.86it/s]
3113505it [00:02, 1089021.18it/s]
3222595it [00:02, 1075225.81it/s]
3330270it [00:03, 1067699.62it/s]
3446341it [00:03, 1095041.66it/s]
3559525it [00:03, 1105909.09it/s]
3671615it [00:03, 1110341.49it/s]
3782727it [00:03, 1098761.12it/s]
3892678it [00:03, 1096082.36it/s]
4013433it [00:03, 1129152.00it/s]
4132257it [00:03, 1146727.03it/s]
4246992it [00:03, 1136232.01it/s]
4360676it [00:03, 1125136.11it/s]
4474835it [00:04, 1129984.11it/s]
4590428it [00:04, 1137634.83it/s]
4704232it [00:04, 1116561.47it/s]
4815991it [00:04, 1111625.57it/s]
4927453it [00:04, 1112484.86it/s]
5038751it [00:04, 1103137.23it/s]
5152712it [00:04, 1113909.95it/s]
5264148it [00:04, 864390.61it/s] 
5359105it [00:05, 802072.02it/s]
5445638it [00:05, 765903.05it/s]
5526538it [00:05, 736838.32it/s]
5603072it [00:05, 717211.27it/s]
5676622it [00:05, 716344.57it/s]
5773980it [00:05, 784776.40it/s]
5876220it [00:05, 850207.74it/s]
5974254it [00:05, 886817.75it/s]
6078878it [00:05, 932619.31it/s]
6179110it [00:05, 952890.86it/s]
6285594it [00:06, 985752.11it/s]
6390368it [00:06, 1004047.93it/s]
6502497it [00:06, 1038829.58it/s]
6607344it [00:06, 1041676.32it/s]
6711802it [00:06, 919051.31it/s] 
6806532it [00:06, 838025.81it/s]
6893323it [00:06, 788645.47it/s]
6974451it [00:06, 757106.56it/s]
7051668it [00:07, 734136.19it/s]
7126024it [00:07, 718933.47it/s]
7198476it [00:07, 710719.14it/s]
7269876it [00:07, 702537.57it/s]
7349511it [00:07, 728718.57it/s]
7443838it [00:07, 789885.24it/s]
7540558it [00:07, 841195.04it/s]
7638520it [00:07, 881675.45it/s]
7742205it [00:07, 927396.87it/s]
7846280it [00:07, 960964.48it/s]
7947198it [00:08, 975284.26it/s]
8049246it [00:08, 988737.13it/s]
8148306it [00:08, 988008.32it/s]
8247237it [00:08, 986866.95it/s]
8347992it [00:08, 992996.00it/s]
8452534it [00:08, 1008661.22it/s]
8553451it [00:08, 1001620.56it/s]
8653962it [00:08, 1002641.09it/s]
8754259it [00:08, 983741.01it/s] 
8855975it [00:08, 993517.57it/s]
8960668it [00:09, 1009333.89it/s]
9061678it [00:09, 1001776.09it/s]
9161917it [00:09, 974465.71it/s] 
9260410it [00:09, 977501.84it/s]
9364648it [00:09, 996563.73it/s]
9472988it [00:09, 1022240.30it/s]
9578991it [00:09, 1033448.58it/s]
9683036it [00:09, 1035510.25it/s]
9786659it [00:09, 1005437.96it/s]
9889642it [00:09, 1012556.86it/s]
9991076it [00:10, 1001400.15it/s]
10091353it [00:10, 981593.47it/s]
10193039it [00:10, 991858.32it/s]
10301655it [00:10, 1019565.08it/s]
10403761it [00:10, 995234.67it/s] 
10503490it [00:10, 980250.76it/s]
10601674it [00:10, 978129.64it/s]
10704123it [00:10, 991699.38it/s]
10803399it [00:10, 967735.24it/s]
10900342it [00:11, 930414.28it/s]
10993726it [00:11, 855971.82it/s]
11080508it [00:11, 759778.97it/s]
11158850it [00:11, 710057.03it/s]
11231679it [00:11, 701228.03it/s]
11319543it [00:11, 747720.71it/s]
11395805it [00:11, 742834.82it/s]
11471099it [00:11, 721389.86it/s]
11543954it [00:11, 704549.77it/s]
11614889it [00:12, 695072.92it/s]
11684698it [00:12, 690675.01it/s]
11777935it [00:12, 759600.74it/s]
11875782it [00:12, 822900.55it/s]
11966772it [00:12, 848334.08it/s]
12061938it [00:12, 878763.74it/s]
12159942it [00:12, 908727.84it/s]
12257146it [00:12, 927482.86it/s]
12352823it [00:12, 936193.84it/s]
12451659it [00:12, 951753.05it/s]
12554622it [00:13, 975022.07it/s]
12653622it [00:13, 979489.26it/s]
12753776it [00:13, 986073.56it/s]
12852431it [00:13, 976787.33it/s]
12950997it [00:13, 979305.78it/s]
13048966it [00:13, 965633.38it/s]
13150794it [00:13, 981114.42it/s]
13249496it [00:13, 982849.11it/s]
13347829it [00:13, 981909.38it/s]
13446057it [00:13, 982000.67it/s]
13544281it [00:14, 980908.85it/s]
13642388it [00:14, 975608.12it/s]
13739965it [00:14, 975253.93it/s]
13837502it [00:14, 902623.71it/s]
13928825it [00:14, 824479.51it/s]
14013080it [00:14, 810000.76it/s]
14109797it [00:14, 852885.21it/s]
14215910it [00:14, 911290.76it/s]
14282442it [00:14, 957150.71it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_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_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bai
+ merge_qc -folders 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1.md -output 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
+ head -n1 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_1q-T1-TRNA-1_B23MHV2LT4_1/659_1q-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv