+ mkdir aih-tih-sc-97ecde-R1_B23WHYVLT4_1
+ all_qc -bam aih-tih-sc-97ecde-R1_B23WHYVLT4_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-97ecde-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_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-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_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-97ecde-R1_B23WHYVLT4_1.md.bai

0it [00:00, ?it/s]
79525it [00:00, 795085.84it/s]
162665it [00:00, 816410.26it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai

248386it [00:00, 834879.39it/s]
341624it [00:00, 873338.67it/s]
435986it [00:00, 898659.03it/s]
525853it [00:00, 897977.41it/s]
619372it [00:00, 910114.37it/s]
719659it [00:00, 939604.44it/s]
813622it [00:00, 935235.09it/s]
914975it [00:01, 959302.53it/s]
1012994it [00:01, 965661.84it/s]
1112107it [00:01, 973376.32it/s]
1209453it [00:01, 947735.45it/s]
1307199it [00:01, 956521.14it/s]
1405218it [00:01, 963539.60it/s]
1514853it [00:01, 1003106.62it/s]
1615268it [00:01, 962121.42it/s] 
1722279it [00:01, 993454.02it/s]
1822020it [00:01, 903876.86it/s]
1914120it [00:02, 890270.26it/s]
2004299it [00:02, 795656.56it/s]
2090080it [00:02, 811898.34it/s]
2192917it [00:02, 870761.77it/s]
2283035it [00:02, 879257.93it/s]
2385070it [00:02, 919535.43it/s]
2478207it [00:02, 909158.09it/s]
2569953it [00:02, 909540.48it/s]
2661489it [00:02, 899590.62it/s]
2759951it [00:03, 924386.36it/s]
2852747it [00:03, 888723.16it/s]
2942116it [00:03, 888982.09it/s]
3031363it [00:03, 867921.99it/s]
3118458it [00:03, 865464.71it/s]
3205519it [00:03, 866942.97it/s]
3301401it [00:03, 893899.75it/s]
3391517it [00:03, 896029.08it/s]
3481237it [00:03, 895408.61it/s]
3570859it [00:03, 869384.73it/s]
3668970it [00:04, 901925.48it/s]
3767786it [00:04, 927294.22it/s]
3876996it [00:04, 976066.45it/s]
3984249it [00:04, 1004715.05it/s]
4094596it [00:04, 1034126.75it/s]
4204596it [00:04, 1053691.15it/s]
4315488it [00:04, 1070185.85it/s]
4424649it [00:04, 1076573.18it/s]
4535845it [00:04, 1087150.42it/s]
4648131it [00:04, 1097822.94it/s]
4760721it [00:05, 1106217.24it/s]
4871365it [00:05, 1104600.13it/s]
4983552it [00:05, 1109734.89it/s]
5094538it [00:05, 1107956.70it/s]
5206168it [00:05, 1110429.91it/s]
5317218it [00:05, 1006320.40it/s]
5419716it [00:05, 983374.49it/s] 
5519356it [00:05, 981321.48it/s]
5618388it [00:05, 982862.44it/s]
5717313it [00:06, 984504.87it/s]
5817117it [00:06, 988397.24it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai

5923741it [00:06, 1011281.00it/s]
6027093it [00:06, 1017725.75it/s]
6129067it [00:06, 999747.15it/s] 
6234290it [00:06, 1015166.47it/s]
6336991it [00:06, 1018645.79it/s]
6438979it [00:06, 1018571.93it/s]
6549779it [00:06, 1045190.84it/s]
6656319it [00:06, 1051202.66it/s]
6762331it [00:07, 1053728.31it/s]
6868916it [00:07, 1057336.97it/s]
6974680it [00:07, 1049984.70it/s]
7084139it [00:07, 1063263.27it/s]
7190496it [00:07, 1062353.53it/s]
7296753it [00:07, 1051971.62it/s]
7404784it [00:07, 1060373.93it/s]
7510854it [00:07, 1058112.35it/s]
7616688it [00:07, 1053176.93it/s]
7722024it [00:07, 1031506.67it/s]
7825272it [00:08, 1002229.63it/s]
7934440it [00:08, 1028130.46it/s]
8044709it [00:08, 1049845.22it/s]
8149909it [00:08, 921643.33it/s] 
8244960it [00:08, 825146.57it/s]
8330916it [00:08, 771794.14it/s]
8410684it [00:08, 734545.01it/s]
8485877it [00:08, 706328.25it/s]
8557596it [00:09, 684222.76it/s]
8626649it [00:09, 667438.42it/s]
8693725it [00:09, 653839.96it/s]
8759258it [00:09, 642211.87it/s]
8823523it [00:09, 638276.33it/s]
8887354it [00:09, 636874.30it/s]
8951035it [00:09, 632828.86it/s]
9014558it [00:09, 633512.37it/s]
9078189it [00:09, 634314.04it/s]
9141751it [00:09, 634685.42it/s]
9205218it [00:10, 632855.50it/s]
9268755it [00:10, 633586.85it/s]
9332113it [00:10, 628994.08it/s]
9396052it [00:10, 632004.51it/s]
9459258it [00:10, 631892.92it/s]
9522562it [00:10, 632186.34it/s]
9586536it [00:10, 634428.09it/s]
9649982it [00:10, 634146.96it/s]
9713399it [00:10, 633021.46it/s]
9777741it [00:10, 636117.48it/s]
9842706it [00:11, 640153.84it/s]
9907258it [00:11, 641712.57it/s]
9972292it [00:11, 644282.65it/s]
10036722it [00:11, 644132.43it/s]
10101573it [00:11, 645419.14it/s]
10166116it [00:11, 643519.37it/s]
10230663it [00:11, 644088.62it/s]
10295658it [00:11, 645829.45it/s]
10361286it [00:11, 648946.16it/s]
10426673it [00:11, 650307.43it/s]
10491705it [00:12, 647628.52it/s]
10556992it [00:12, 649180.99it/s]
10622104it [00:12, 649747.57it/s]
10687168it [00:12, 649998.79it/s]
10752170it [00:12, 647487.15it/s]
10817126it [00:12, 648092.66it/s]
10882028it [00:12, 648272.29it/s]
10925498it [00:12, 858549.44it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_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-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md.bai
+ merge_qc -folders aih-tih-sc-97ecde-R1_B23WHYVLT4_1/aih-tih-sc-97ecde-R1_B23WHYVLT4_1.md -output aih-tih-sc-97ecde-R1_B23WHYVLT4_1/aih-tih-sc-97ecde-R1_B23WHYVLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-97ecde-R1_B23WHYVLT4_1/aih-tih-sc-97ecde-R1_B23WHYVLT4_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-97ecde-R1_B23WHYVLT4_1/aih-tih-sc-97ecde-R1_B23WHYVLT4_1_full_basic_stats.tsv