+ mkdir tih_rna_sample_00572_B23MVV7LT4_1
+ all_qc -bam tih_rna_sample_00572_B23MVV7LT4_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 tih_rna_sample_00572_B23MVV7LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.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_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_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: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
0it [00:00, ?it/s]
121392it [00:00, 1213814.08it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
256854it [00:00, 1296337.06it/s]
394592it [00:00, 1333301.87it/s]
527923it [00:00, 1317274.31it/s]
659680it [00:00, 1310082.77it/s]
794123it [00:00, 1321627.63it/s]
929774it [00:00, 1332930.89it/s]
1063429it [00:00, 1334050.50it/s]
1198251it [00:00, 1338307.84it/s]
1332727it [00:01, 1340151.38it/s]
1468711it [00:01, 1346142.04it/s]
1603333it [00:01, 1345665.96it/s]
1737905it [00:01, 1320758.54it/s]
1870084it [00:01, 1307837.23it/s]
2000952it [00:01, 1298484.52it/s]
2136188it [00:01, 1314328.64it/s]
2267689it [00:01, 1289688.75it/s]
2398548it [00:01, 1295212.83it/s]
2528169it [00:01, 1294317.00it/s]
2660864it [00:02, 1303788.33it/s]
2795922it [00:02, 1317694.67it/s]
2930952it [00:02, 1327395.73it/s]
3063734it [00:02, 1320406.75it/s]
3199788it [00:02, 1332337.42it/s]
3333055it [00:02, 1229884.72it/s]
3457595it [00:02, 1071439.47it/s]
3569066it [00:02, 993966.09it/s]
3671979it [00:02, 939431.24it/s]
3768404it [00:03, 871560.74it/s]
3857561it [00:03, 849389.32it/s]
3943686it [00:03, 833093.24it/s]
4027672it [00:03, 820499.72it/s]
4110091it [00:03, 820330.98it/s]
4192381it [00:03, 816959.77it/s]
4274236it [00:03, 813974.59it/s]
4355731it [00:03, 803643.19it/s]
4438875it [00:03, 811645.89it/s]
4520213it [00:04, 811992.83it/s]
4601464it [00:04, 803980.11it/s]
4682263it [00:04, 805140.95it/s]
4762807it [00:04, 801535.96it/s]
4843371it [00:04, 802734.99it/s]
4924506it [00:04, 805277.01it/s]
5006967it [00:04, 811017.20it/s]
5088082it [00:04, 807703.07it/s]
5168864it [00:04, 805895.85it/s]
5249461it [00:04, 802741.89it/s]
5329742it [00:05, 796708.29it/s]
5409424it [00:05, 791321.66it/s]
5488567it [00:05, 790176.18it/s]
5567592it [00:05, 786911.47it/s]
5646492it [00:05, 787517.80it/s]
5725396it [00:05, 787954.29it/s]
5806039it [00:05, 793452.58it/s]
5887318it [00:05, 799215.49it/s]
5967245it [00:05, 795156.30it/s]
6049557it [00:05, 803478.53it/s]
6131051it [00:06, 806886.75it/s]
6211748it [00:06, 802745.05it/s]
6292032it [00:06, 801912.79it/s]
6375178it [00:06, 810687.16it/s]
6459409it [00:06, 820124.84it/s]
6541431it [00:06, 817939.58it/s]
6623233it [00:06, 812510.81it/s]
6704496it [00:06, 805838.27it/s]
6785096it [00:06, 802173.94it/s]
6865325it [00:06, 800654.13it/s]
6945972it [00:07, 802317.01it/s]
7026793it [00:07, 804051.11it/s]
7107204it [00:07, 803310.44it/s]
7188175it [00:07, 805206.64it/s]
7269245it [00:07, 806740.00it/s]
7353286it [00:07, 816805.68it/s]
7489167it [00:07, 979157.33it/s]
7627049it [00:07, 1098901.83it/s]
7763929it [00:07, 1179791.82it/s]
7903571it [00:07, 1244717.02it/s]
8040932it [00:08, 1283343.21it/s]
8180310it [00:08, 1316440.93it/s]
8323178it [00:08, 1350079.02it/s]
8462058it [00:08, 1361608.17it/s]
8602205it [00:08, 1373433.64it/s]
8742816it [00:08, 1383194.67it/s]
8881139it [00:08, 1370793.73it/s]
9022454it [00:08, 1383386.28it/s]
9161079it [00:08, 1384218.26it/s]
9299521it [00:08, 1379679.22it/s]
9437505it [00:09, 1373742.57it/s]
9574894it [00:09, 1370189.18it/s]
9711923it [00:09, 1358053.44it/s]
9848570it [00:09, 1360526.14it/s]
9988386it [00:09, 1371622.79it/s]
10127996it [00:09, 1378735.40it/s]
10267319it [00:09, 1383046.01it/s]
10406351it [00:09, 1385200.06it/s]
10545190it [00:09, 1386134.86it/s]
10684013it [00:09, 1386740.18it/s]
10822693it [00:10, 1382989.28it/s]
10960998it [00:10, 1377049.47it/s]
11101915it [00:10, 1386617.95it/s]
11242838it [00:10, 1393358.15it/s]
11382184it [00:10, 1272746.55it/s]
11511475it [00:10, 1094083.88it/s]
11650063it [00:10, 1168645.04it/s]
11785938it [00:10, 1219374.44it/s]
11925601it [00:10, 1268358.92it/s]
12067509it [00:11, 1311010.78it/s]
12208937it [00:11, 1340728.67it/s]
12349313it [00:11, 1359080.33it/s]
12486843it [00:11, 1098497.38it/s]
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_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: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00572_B23MVV7LT4_1.md.bai
+ merge_qc -folders tih_rna_sample_00572_B23MVV7LT4_1/tih_rna_sample_00572_B23MVV7LT4_1.md -output tih_rna_sample_00572_B23MVV7LT4_1/tih_rna_sample_00572_B23MVV7LT4_1_full_basic_stats.tsv
+ head -n1 tih_rna_sample_00572_B23MVV7LT4_1/tih_rna_sample_00572_B23MVV7LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00572_B23MVV7LT4_1/tih_rna_sample_00572_B23MVV7LT4_1_full_basic_stats.tsv