+ mkdir aih-tih-sc-3282fd-R1_A23YTGFLT4_1
+ all_qc -bam aih-tih-sc-3282fd-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-3282fd-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-3282fd-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-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1.md.bai

0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai

105148it [00:00, 1002151.17it/s]
218736it [00:00, 1079174.45it/s]
360239it [00:00, 1230802.73it/s]
508466it [00:00, 1329363.91it/s]
652782it [00:00, 1370169.60it/s]
798356it [00:00, 1398955.56it/s]
938363it [00:00, 1346471.83it/s]
1073455it [00:00, 1319204.35it/s]
1209443it [00:00, 1331447.70it/s]
1342873it [00:01, 1263423.90it/s]
1469995it [00:01, 1206614.35it/s]
1591497it [00:01, 1159731.75it/s]
1708177it [00:01, 1134499.09it/s]
1822064it [00:01, 1117620.80it/s]
1934074it [00:01, 1108826.59it/s]
2045092it [00:01, 1104618.76it/s]
2155631it [00:01, 1097665.56it/s]
2265435it [00:01, 1086289.78it/s]
2374083it [00:02, 1044757.28it/s]
2484550it [00:02, 1061855.29it/s]
2592783it [00:02, 1067764.20it/s]
2713716it [00:02, 1109206.94it/s]
2847260it [00:02, 1175916.98it/s]
2991091it [00:02, 1253678.60it/s]
3138194it [00:02, 1318295.66it/s]
3275092it [00:02, 1333379.82it/s]
3408620it [00:02, 1296653.00it/s]
3550991it [00:02, 1333870.99it/s]
3689608it [00:03, 1349270.34it/s]
3829535it [00:03, 1364051.15it/s]
3966135it [00:03, 1219598.31it/s]
4091036it [00:03, 1127186.80it/s]
4206771it [00:03, 1064268.64it/s]
4315536it [00:03, 1047355.14it/s]
4423613it [00:03, 1056287.64it/s]
4559988it [00:03, 1141419.71it/s]
4697460it [00:03, 1207533.93it/s]
4828255it [00:04, 1236161.19it/s]
4961087it [00:04, 1263003.95it/s]
5106633it [00:04, 1319518.39it/s]
5259170it [00:04, 1380379.63it/s]
5405241it [00:04, 1404203.14it/s]
5546097it [00:04, 1288102.44it/s]
5677055it [00:04, 1219756.12it/s]
5801000it [00:04, 1172001.45it/s]
5919668it [00:04, 1148648.15it/s]
6035476it [00:05, 1128375.86it/s]
6148904it [00:05, 1115138.84it/s]
6260775it [00:05, 1105434.36it/s]
6374244it [00:05, 1113502.95it/s]
6485785it [00:05, 1074657.97it/s]
6593563it [00:05, 1050906.32it/s]
6698884it [00:05, 1030093.27it/s]
6802050it [00:05, 1015093.80it/s]
6903647it [00:05, 1010095.05it/s]
7004700it [00:05, 1005093.07it/s]
7105228it [00:06, 1001715.23it/s]
7205405it [00:06, 996609.93it/s] 
7305829it [00:06, 998818.99it/s]
7405714it [00:06, 995161.85it/s]
7505231it [00:06, 991548.83it/s]
7604385it [00:06, 983242.91it/s]
7724971it [00:06, 1049076.13it/s]
7863221it [00:06, 1148106.97it/s]
8000500it [00:06, 1215006.78it/s]
8144386it [00:06, 1281801.44it/s]
8285647it [00:07, 1320878.52it/s]
8435295it [00:07, 1373395.21it/s]
8582255it [00:07, 1402161.10it/s]
8733371it [00:07, 1434778.58it/s]
8887950it [00:07, 1467883.59it/s]
9036179it [00:07, 1472016.73it/s]
9183408it [00:07, 1465056.04it/s]
9334388it [00:07, 1478387.15it/s]
9482250it [00:07, 1469023.64it/s]
9629180it [00:07, 1448487.91it/s]
9774102it [00:08, 1441478.87it/s]
9918299it [00:08, 1422435.70it/s]
10060610it [00:08, 1366783.97it/s]
10210684it [00:08, 1405293.83it/s]
10357567it [00:08, 1423769.62it/s]
10510879it [00:08, 1455863.17it/s]
10659551it [00:08, 1464808.42it/s]
10806278it [00:08, 1457722.51it/s]
10952224it [00:08, 1453094.38it/s]
11110767it [00:08, 1492360.94it/s]
11269778it [00:09, 1521435.13it/s]
11422030it [00:09, 1514207.47it/s]
11573531it [00:09, 1473439.00it/s]
11721149it [00:09, 1467429.47it/s]
11874905it [00:09, 1488006.56it/s]
12034231it [00:09, 1519088.39it/s]
12162132it [00:09, 1254997.41it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai
+ merge_qc -folders aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md -output aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1_full_basic_stats.tsv