+ mkdir 659_bIB-T1-TRNA-1_B23MHV2LT4_1
+ all_qc -bam 659_bIB-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_bIB-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_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
0it [00:00, ?it/s]
124590it [00:00, 1245832.87it/s]
256914it [00:00, 1291333.59it/s]
392364it [00:00, 1320119.06it/s]
527233it [00:00, 1331371.01it/s]
660371it [00:00, 1310708.40it/s]
791498it [00:00, 1136297.10it/s]
926403it [00:00, 1198854.23it/s]
1049356it [00:00, 1176046.92it/s]
1184091it [00:00, 1225970.71it/s]
1320551it [00:01, 1266715.70it/s]
1455015it [00:01, 1289715.87it/s]
1594990it [00:01, 1322338.81it/s]
1730155it [00:01, 1330960.54it/s]
1867611it [00:01, 1343954.89it/s]
2003749it [00:01, 1349010.75it/s]
2139559it [00:01, 1351580.60it/s]
2274930it [00:01, 1306099.47it/s]
2412335it [00:01, 1325952.54it/s]
2545313it [00:01, 1323416.94it/s]
2683042it [00:02, 1339240.54it/s]
2822221it [00:02, 1354827.55it/s]
2960139it [00:02, 1362064.48it/s]
3097477it [00:02, 1365427.73it/s]
3238082it [00:02, 1377556.65it/s]
3375903it [00:02, 1367887.76it/s]
3512751it [00:02, 1327121.50it/s]
3645747it [00:02, 1315717.18it/s]
3784355it [00:02, 1336289.90it/s]
3926796it [00:02, 1362242.19it/s]
4075695it [00:03, 1399706.73it/s]
4223662it [00:03, 1423461.50it/s]
4369750it [00:03, 1434590.66it/s]
4515564it [00:03, 1441494.24it/s]
4663277it [00:03, 1452127.81it/s]
4812116it [00:03, 1462959.40it/s]
4959998it [00:03, 1467686.65it/s]
5106797it [00:03, 1383770.49it/s]
5246177it [00:03, 1339692.33it/s]
5381014it [00:04, 1291635.11it/s]
5510956it [00:04, 1240248.29it/s]
5635702it [00:04, 1214364.65it/s]
5757591it [00:04, 1191104.41it/s]
5893405it [00:04, 1237967.01it/s]
6019486it [00:04, 1244333.52it/s]
6144300it [00:04, 1237025.68it/s]
6280902it [00:04, 1274655.93it/s]
6418865it [00:04, 1305525.97it/s]
6556361it [00:04, 1326051.59it/s]
6693940it [00:05, 1340814.44it/s]
6832944it [00:05, 1355465.45it/s]
6971064it [00:05, 1363100.43it/s]
7107464it [00:05, 1356069.15it/s]
7243140it [00:05, 1352572.57it/s]
7378446it [00:05, 1189632.59it/s]
7519909it [00:05, 1250926.86it/s]
7657802it [00:05, 1286780.63it/s]
7795517it [00:05, 1312598.04it/s]
7928605it [00:06, 1304317.18it/s]
8060309it [00:06, 1204565.36it/s]
8183004it [00:06, 1179714.63it/s]
8302502it [00:06, 1181295.31it/s]
8421712it [00:06, 1163292.94it/s]
8541362it [00:06, 1172734.67it/s]
8659201it [00:06, 1172268.95it/s]
8795199it [00:06, 1227064.39it/s]
8931933it [00:06, 1268146.33it/s]
9069939it [00:06, 1301258.82it/s]
9202044it [00:07, 1307126.79it/s]
9332978it [00:07, 1252740.80it/s]
9458865it [00:07, 1229233.35it/s]
9596070it [00:07, 1270422.07it/s]
9733184it [00:07, 1299802.29it/s]
9870790it [00:07, 1322227.64it/s]
10007920it [00:07, 1336734.01it/s]
10146075it [00:07, 1350036.20it/s]
10282361it [00:07, 1353843.62it/s]
10417883it [00:07, 1349500.42it/s]
10554426it [00:08, 1354238.76it/s]
10693132it [00:08, 1364031.23it/s]
10831703it [00:08, 1370503.14it/s]
10968793it [00:08, 1368385.49it/s]
11107786it [00:08, 1374819.10it/s]
11247046it [00:08, 1380130.45it/s]
11385075it [00:08, 1378758.39it/s]
11525084it [00:08, 1385131.21it/s]
11665246it [00:08, 1390056.77it/s]
11804259it [00:08, 1390007.60it/s]
11944216it [00:09, 1392856.09it/s]
12083506it [00:09, 1390343.83it/s]
12222544it [00:09, 1389152.71it/s]
12361462it [00:09, 1375436.24it/s]
12499226it [00:09, 1376076.77it/s]
12636856it [00:09, 1372662.61it/s]
12775189it [00:09, 1375828.12it/s]
12912785it [00:09, 1374105.00it/s]
13050205it [00:09, 1372120.60it/s]
13188324it [00:09, 1374813.29it/s]
13325811it [00:10, 1372323.31it/s]
13465118it [00:10, 1378393.94it/s]
13603168it [00:10, 1379010.97it/s]
13741402it [00:10, 1379994.72it/s]
13880776it [00:10, 1384101.30it/s]
14021839it [00:10, 1392041.20it/s]
14161046it [00:10, 1389853.48it/s]
14300034it [00:10, 1386959.50it/s]
14438733it [00:10, 1381520.27it/s]
14578785it [00:11, 1387184.04it/s]
14719178it [00:11, 1392178.44it/s]
14858402it [00:11, 1390449.79it/s]
14997778it [00:11, 1391409.06it/s]
15136923it [00:11, 1387904.67it/s]
15275718it [00:11, 1385538.37it/s]
15414275it [00:11, 1376794.97it/s]
15551967it [00:11, 1373379.57it/s]
15691739it [00:11, 1380615.23it/s]
15831291it [00:11, 1385036.15it/s]
15971302it [00:12, 1389468.93it/s]
16110257it [00:12, 1382224.89it/s]
16248948it [00:12, 1383606.69it/s]
16387319it [00:12, 1381993.31it/s]
16525525it [00:12, 1331870.84it/s]
16659094it [00:12, 1208107.65it/s]
16794129it [00:12, 1246978.16it/s]
16932337it [00:12, 1284823.81it/s]
17071094it [00:12, 1314261.79it/s]
17208410it [00:12, 1331358.60it/s]
17346505it [00:13, 1345755.01it/s]
17483519it [00:13, 1352937.27it/s]
17623409it [00:13, 1366559.68it/s]
17760429it [00:13, 1356669.82it/s]
17896362it [00:13, 1344811.13it/s]
18032114it [00:13, 1348553.48it/s]
18167114it [00:13, 1335698.47it/s]
18284246it [00:13, 1329476.04it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai
+ merge_qc -folders 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
+ head -n1 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv