+ mkdir tih_rna_sample_00599_B23MVV7LT4_1
+ all_qc -bam tih_rna_sample_00599_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_00599_B23MVV7LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_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_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_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_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
0it [00:00, ?it/s]
91184it [00:00, 911469.27it/s]
211063it [00:00, 1080399.23it/s]
323419it [00:00, 1100073.16it/s]
472382it [00:00, 1253806.59it/s]
602174it [00:00, 1269678.44it/s]
750218it [00:00, 1341292.66it/s]
885275it [00:00, 1344018.93it/s]
1028945it [00:00, 1373441.52it/s]
1177844it [00:00, 1409512.59it/s]
1318796it [00:01, 1390938.11it/s]
1457944it [00:01, 1310851.90it/s]
1606401it [00:01, 1361110.93it/s]
1748495it [00:01, 1378591.60it/s]
1887028it [00:01, 1339041.33it/s]
2035217it [00:01, 1380431.46it/s]
2189422it [00:01, 1427663.29it/s]
2332745it [00:01, 1419010.83it/s]
2478767it [00:01, 1431111.86it/s]
2622172it [00:01, 1421221.01it/s]
2772798it [00:02, 1446360.34it/s]
2921145it [00:02, 1457365.22it/s]
3073400it [00:02, 1476763.22it/s]
3221188it [00:02, 1433357.52it/s]
3364864it [00:02, 1430502.98it/s]
3508147it [00:02, 1421452.83it/s]
3659054it [00:02, 1446621.03it/s]
3818356it [00:02, 1489933.10it/s]
3967740it [00:02, 1491065.27it/s]
4116964it [00:02, 1478781.99it/s]
4276155it [00:03, 1512342.73it/s]
4427494it [00:03, 1455813.66it/s]
4588028it [00:03, 1499159.63it/s]
4744510it [00:03, 1518384.51it/s]
4896734it [00:03, 1503415.74it/s]
5047359it [00:03, 1428935.23it/s]
5191124it [00:03, 1425803.43it/s]
5334301it [00:03, 1426583.24it/s]
5477380it [00:03, 1337635.18it/s]
5612408it [00:04, 1265581.21it/s]
5740334it [00:04, 1239480.58it/s]
5865166it [00:04, 1234570.90it/s]
5989209it [00:04, 1223517.42it/s]
6111932it [00:04, 1218588.77it/s]
6234032it [00:04, 1216596.46it/s]
6357094it [00:04, 1220662.66it/s]
6479286it [00:04, 1217298.43it/s]
6601099it [00:04, 1204544.37it/s]
6721862it [00:04, 1205414.81it/s]
6842454it [00:05, 1195134.12it/s]
6976376it [00:05, 1237667.63it/s]
7122938it [00:05, 1305288.13it/s]
7253608it [00:05, 1291561.67it/s]
7382887it [00:05, 1254888.67it/s]
7508651it [00:05, 1227848.39it/s]
7631690it [00:05, 1215753.33it/s]
7764602it [00:05, 1248632.44it/s]
7910821it [00:05, 1311046.53it/s]
8050989it [00:05, 1337764.18it/s]
8198562it [00:06, 1378647.46it/s]
8350343it [00:06, 1420033.77it/s]
8497125it [00:06, 1434262.54it/s]
8641945it [00:06, 1438395.60it/s]
8785887it [00:06, 1435103.63it/s]
8929470it [00:06, 1408133.67it/s]
9070440it [00:06, 1295735.41it/s]
9201775it [00:06, 1221629.55it/s]
9325705it [00:06, 1179399.50it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
9444891it [00:07, 1155754.02it/s]
9561251it [00:07, 1089980.63it/s]
9671173it [00:07, 1083875.22it/s]
9780832it [00:07, 1087373.24it/s]
9890014it [00:07, 1059809.92it/s]
9996330it [00:07, 1035841.93it/s]
10100146it [00:07, 1034097.10it/s]
10203709it [00:07, 1002069.01it/s]
10306886it [00:07, 1010498.84it/s]
10408642it [00:08, 1012518.02it/s]
10510036it [00:08, 986365.16it/s]
10616715it [00:08, 1009586.10it/s]
10729100it [00:08, 1042950.87it/s]
10874950it [00:08, 1165307.56it/s]
11025415it [00:08, 1265740.21it/s]
11179573it [00:08, 1347709.24it/s]
11314706it [00:08, 1325408.27it/s]
11447574it [00:08, 1295118.72it/s]
11577428it [00:08, 1278333.38it/s]
11705508it [00:09, 1253862.90it/s]
11831108it [00:09, 1249330.70it/s]
11956179it [00:09, 1248452.33it/s]
12098538it [00:09, 1299918.38it/s]
12234392it [00:09, 1317190.29it/s]
12369376it [00:09, 1326864.98it/s]
12519999it [00:09, 1380276.15it/s]
12675591it [00:09, 1432608.38it/s]
12832887it [00:09, 1474462.36it/s]
12984819it [00:09, 1487799.48it/s]
13133664it [00:10, 1469444.68it/s]
13280703it [00:10, 1445861.75it/s]
13425420it [00:10, 1367195.62it/s]
13563012it [00:10, 1289399.50it/s]
13693193it [00:10, 1233625.27it/s]
13817602it [00:10, 1225085.49it/s]
13940784it [00:10, 1225551.79it/s]
14063814it [00:10, 1222422.14it/s]
14186376it [00:10, 1200181.33it/s]
14306633it [00:11, 1189429.07it/s]
14430339it [00:11, 1203194.80it/s]
14553204it [00:11, 1210610.86it/s]
14675984it [00:11, 1215656.61it/s]
14797647it [00:11, 1176998.36it/s]
14940767it [00:11, 1250860.44it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
15089819it [00:11, 1321146.15it/s]
15232648it [00:11, 1352663.56it/s]
15380671it [00:11, 1390485.66it/s]
15520026it [00:11, 1385583.51it/s]
15661108it [00:12, 1393050.16it/s]
15801510it [00:12, 1396297.35it/s]
15941252it [00:12, 1388179.90it/s]
16080157it [00:12, 1373232.12it/s]
16227341it [00:12, 1402417.15it/s]
16367682it [00:12, 1396558.97it/s]
16531357it [00:12, 1467871.09it/s]
16685374it [00:12, 1489393.09it/s]
16837359it [00:12, 1498462.72it/s]
16988814it [00:12, 1503240.40it/s]
17147622it [00:13, 1528609.20it/s]
17321376it [00:13, 1591162.40it/s]
17480532it [00:13, 1532265.24it/s]
17634250it [00:13, 1505257.71it/s]
17790135it [00:13, 1520652.99it/s]
17942523it [00:13, 1468106.41it/s]
18089858it [00:13, 1457685.89it/s]
18249737it [00:13, 1498118.90it/s]
18399931it [00:13, 1487103.15it/s]
18550315it [00:14, 1491862.54it/s]
18699696it [00:14, 1472961.72it/s]
18852089it [00:14, 1487774.16it/s]
19001011it [00:14, 1427084.60it/s]
19144492it [00:14, 1429290.28it/s]
19287823it [00:14, 1384800.02it/s]
19426787it [00:14, 1320738.20it/s]
19559620it [00:14, 1284206.11it/s]
19688599it [00:14, 1269378.98it/s]
19815876it [00:14, 1259567.81it/s]
19942035it [00:15, 1244642.44it/s]
20066617it [00:15, 1235504.11it/s]
20191080it [00:15, 1238124.74it/s]
20314945it [00:15, 1229145.29it/s]
20437891it [00:15, 1226784.52it/s]
20560587it [00:15, 1226138.25it/s]
20625676it [00:15, 1319288.66it/s]
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_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_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00599_B23MVV7LT4_1.md.bai
+ merge_qc -folders tih_rna_sample_00599_B23MVV7LT4_1/tih_rna_sample_00599_B23MVV7LT4_1.md -output tih_rna_sample_00599_B23MVV7LT4_1/tih_rna_sample_00599_B23MVV7LT4_1_full_basic_stats.tsv
+ head -n1 tih_rna_sample_00599_B23MVV7LT4_1/tih_rna_sample_00599_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_00599_B23MVV7LT4_1/tih_rna_sample_00599_B23MVV7LT4_1_full_basic_stats.tsv