+ mkdir tih_rna_sample_00161_B23WHTKLT4_2
+ all_qc -bam tih_rna_sample_00161_B23WHTKLT4_2.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 tih_rna_sample_00161_B23WHTKLT4_2 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.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: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
108013it [00:00, 1080056.35it/s]
220918it [00:00, 1108837.08it/s]
334503it [00:00, 1121142.52it/s]
448340it [00:00, 1127918.44it/s]
562731it [00:00, 1133596.60it/s]
676091it [00:00, 1133077.37it/s]
789399it [00:00, 1128620.99it/s]
902676it [00:00, 1129887.01it/s]
1016734it [00:00, 1133204.75it/s]
1130113it [00:01, 1133364.68it/s]
1243452it [00:01, 1130806.69it/s]
1356668it [00:01, 1131194.04it/s]
1470874it [00:01, 1134462.78it/s]
1585017it [00:01, 1136544.73it/s]
1699645it [00:01, 1139390.49it/s]
1814534it [00:01, 1142229.58it/s]
1928758it [00:01, 1140382.88it/s]
2042822it [00:01, 1140436.70it/s]
2156867it [00:01, 1140214.27it/s]
2271024it [00:02, 1140601.71it/s]
2385085it [00:02, 1138818.32it/s]
2498968it [00:02, 1126589.47it/s]
2611656it [00:02, 1121843.03it/s]
2725300it [00:02, 1126163.75it/s]
2840953it [00:02, 1135197.12it/s]
2957115it [00:02, 1142996.03it/s]
3071432it [00:02, 1138296.29it/s]
3185277it [00:02, 1135974.77it/s]
3298885it [00:02, 1132959.57it/s]
3412233it [00:03, 1132991.05it/s]
3525538it [00:03, 1131104.64it/s]
3641000it [00:03, 1138112.72it/s]
3754817it [00:03, 1098020.70it/s]
3864919it [00:03, 1080941.79it/s]
3973243it [00:03, 1051455.01it/s]
4078651it [00:03, 1038850.29it/s]
4190335it [00:03, 1061307.56it/s]
4302770it [00:03, 1079695.44it/s]
4417121it [00:03, 1098461.76it/s]
4531631it [00:04, 1112249.41it/s]
4646705it [00:04, 1123674.51it/s]
4762550it [00:04, 1133923.64it/s]
4876122it [00:04, 1134371.51it/s]
4989617it [00:04, 1134256.14it/s]
5103084it [00:04, 1114500.84it/s]
5214636it [00:04, 1091948.29it/s]
5323977it [00:04, 1072729.24it/s]
5431386it [00:04, 1043424.13it/s]
5535925it [00:04, 992397.57it/s]
5648617it [00:05, 1030192.09it/s]
5761874it [00:05, 1059507.78it/s]
5871629it [00:05, 1070536.40it/s]
5983359it [00:05, 1084186.16it/s]
6095940it [00:05, 1096455.16it/s]
6210497it [00:05, 1111000.87it/s]
6322796it [00:05, 1114548.15it/s]
6435535it [00:05, 1118269.84it/s]
6548805it [00:05, 1122563.65it/s]
6663430it [00:05, 1129523.56it/s]
6777393it [00:06, 1132531.87it/s]
6890823it [00:06, 1133017.36it/s]
7004151it [00:06, 1132167.72it/s]
7118850it [00:06, 1136581.36it/s]
7233891it [00:06, 1140634.34it/s]
7347964it [00:06, 1138900.96it/s]
7461862it [00:06, 1134243.98it/s]
7575296it [00:06, 1133106.54it/s]
7688982it [00:06, 1134190.15it/s]
7802407it [00:06, 1134188.96it/s]
7915830it [00:07, 1131773.26it/s]
8030318it [00:07, 1135673.83it/s]
8143889it [00:07, 1130026.76it/s]
8256900it [00:07, 1129948.18it/s]
8371062it [00:07, 1133420.18it/s]
8484791it [00:07, 1134556.77it/s]
8598251it [00:07, 1130317.54it/s]
8711289it [00:07, 1118013.83it/s]
8823952it [00:07, 1120550.89it/s]
8936031it [00:08, 1115794.26it/s]
9048067it [00:08, 1117133.38it/s]
9162043it [00:08, 1123864.61it/s]
9275647it [00:08, 1127481.22it/s]
9390052it [00:08, 1132417.95it/s]
9506548it [00:08, 1142140.27it/s]
9620771it [00:08, 1141538.85it/s]
9736044it [00:08, 1144872.30it/s]
9850949it [00:08, 1146106.70it/s]
9965772it [00:08, 1146722.27it/s]
10080447it [00:09, 1144244.94it/s]
10196240it [00:09, 1148319.35it/s]
10311075it [00:09, 1123148.58it/s]
10423512it [00:09, 1110697.00it/s]
10534680it [00:09, 1104672.35it/s]
10645213it [00:09, 1094222.84it/s]
10754686it [00:09, 1085951.51it/s]
10864393it [00:09, 1089204.66it/s]
10975624it [00:09, 1095892.21it/s]
11086400it [00:09, 1099399.84it/s]
11196365it [00:10, 1088644.94it/s]
11305264it [00:10, 1083399.63it/s]
11413629it [00:10, 1073366.73it/s]
11520993it [00:10, 1068617.05it/s]
11632175it [00:10, 1081387.57it/s]
11740344it [00:10, 1076660.55it/s]
11848032it [00:10, 1076398.22it/s]
11955687it [00:10, 1071776.87it/s]
12064503it [00:10, 1076630.00it/s]
12176308it [00:10, 1088966.47it/s]
12286208it [00:11, 1091947.07it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
12402053it [00:11, 1111825.42it/s]
12513250it [00:11, 1103105.39it/s]
12624059it [00:11, 1104565.67it/s]
12734534it [00:11, 1092031.23it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
12843777it [00:11, 1088377.22it/s]
12952641it [00:11, 1083943.49it/s]
13061054it [00:11, 1077593.19it/s]
13169095it [00:11, 1078407.64it/s]
13283833it [00:11, 1098918.13it/s]
13396263it [00:12, 1106416.50it/s]
13509747it [00:12, 1114889.43it/s]
13621255it [00:12, 1104742.56it/s]
13731761it [00:12, 1087637.57it/s]
13840594it [00:12, 1082848.88it/s]
13952333it [00:12, 1093036.79it/s]
14064081it [00:12, 1100271.58it/s]
14178623it [00:12, 1113648.57it/s]
14291834it [00:12, 1119139.90it/s]
14404837it [00:12, 1122372.78it/s]
14517097it [00:13, 1119873.39it/s]
14629101it [00:13, 1070419.20it/s]
14741193it [00:13, 1084984.73it/s]
14853423it [00:13, 1095896.14it/s]
14966007it [00:13, 1104708.80it/s]
15078506it [00:13, 1110663.18it/s]
15191718it [00:13, 1117026.04it/s]
15305733it [00:13, 1123902.72it/s]
15419239it [00:13, 1127213.88it/s]
15532022it [00:13, 1126402.38it/s]
15645157it [00:14, 1127862.93it/s]
15758069it [00:14, 1128221.94it/s]
15870913it [00:14, 1116950.20it/s]
15982648it [00:14, 1082250.18it/s]
16091113it [00:14, 1045264.12it/s]
16197391it [00:14, 1050269.00it/s]
16305377it [00:14, 1058850.25it/s]
16411482it [00:14, 1048088.35it/s]
16516449it [00:14, 1020648.25it/s]
16618729it [00:15, 1010421.65it/s]
16730309it [00:15, 1041010.56it/s]
16844524it [00:15, 1070650.48it/s]
16958100it [00:15, 1089758.80it/s]
17068374it [00:15, 1093589.42it/s]
17181670it [00:15, 1105289.12it/s]
17292298it [00:15, 1073896.27it/s]
17405645it [00:15, 1091315.80it/s]
17519660it [00:15, 1105698.52it/s]
17632529it [00:15, 1112491.63it/s]
17747177it [00:16, 1122580.22it/s]
17860953it [00:16, 1127092.25it/s]
17976076it [00:16, 1134272.21it/s]
18089558it [00:16, 1125649.37it/s]
18203832it [00:16, 1130707.99it/s]
18317742it [00:16, 1133192.49it/s]
18432199it [00:16, 1136567.49it/s]
18545878it [00:16, 1132937.59it/s]
18659189it [00:16, 1131489.49it/s]
18773314it [00:16, 1134313.07it/s]
18846867it [00:16, 1108877.44it/s]
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.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: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai
+ merge_qc -folders tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md -output tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2_full_basic_stats.tsv
+ head -n1 tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2_full_basic_stats.tsv