+ mkdir tih_rna_sample_00089_23H5VFLT4_s39
+ all_qc -bam tih_rna_sample_00089_23H5VFLT4_s39.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_00089_23H5VFLT4_s39 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.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_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.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_00089_23H5VFLT4_s39.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
99400it [00:00, 993704.80it/s]
214967it [00:00, 1088907.85it/s]
331376it [00:00, 1123068.53it/s]
446663it [00:00, 1134790.86it/s]
577673it [00:00, 1197927.45it/s]
702126it [00:00, 1209391.13it/s]
839982it [00:00, 1264516.66it/s]
970158it [00:00, 1276304.63it/s]
1107860it [00:00, 1307716.75it/s]
1238641it [00:01, 1276506.77it/s]
1366454it [00:01, 1273895.94it/s]
1493954it [00:01, 1165935.14it/s]
1612285it [00:01, 1110946.98it/s]
1724859it [00:01, 1097733.63it/s]
1835598it [00:01, 1073846.71it/s]
1943624it [00:01, 1064448.85it/s]
2084619it [00:01, 1162470.70it/s]
2226722it [00:01, 1237070.39it/s]
2357502it [00:01, 1257510.17it/s]
2491629it [00:02, 1282130.98it/s]
2631496it [00:02, 1316539.98it/s]
2774295it [00:02, 1349497.73it/s]
2933052it [00:02, 1420398.15it/s]
3075371it [00:02, 1347027.91it/s]
3211038it [00:02, 1298904.81it/s]
3345464it [00:02, 1311733.36it/s]
3503641it [00:02, 1389545.10it/s]
3654359it [00:02, 1423821.38it/s]
3797406it [00:03, 1416863.78it/s]
3939554it [00:03, 1416682.80it/s]
4081545it [00:03, 1383366.64it/s]
4220246it [00:03, 1343968.34it/s]
4355059it [00:03, 1293092.83it/s]
4488625it [00:03, 1305128.48it/s]
4639532it [00:03, 1363901.87it/s]
4776476it [00:03, 1304374.48it/s]
4907733it [00:03, 1226853.51it/s]
5045365it [00:03, 1267986.70it/s]
5189931it [00:04, 1318243.32it/s]
5322912it [00:04, 1316900.37it/s]
5475589it [00:04, 1377820.57it/s]
5632139it [00:04, 1432856.25it/s]
5791281it [00:04, 1479653.06it/s]
5939777it [00:04, 1452466.81it/s]
6085487it [00:04, 1341416.60it/s]
6221491it [00:04, 1292256.83it/s]
6352150it [00:04, 1284196.83it/s]
6481526it [00:05, 1249314.11it/s]
6613563it [00:05, 1269228.51it/s]
6756633it [00:05, 1315411.63it/s]
6888834it [00:05, 1296137.16it/s]
7018920it [00:05, 1210861.37it/s]
7141277it [00:05, 1019590.17it/s]
7260836it [00:05, 1063652.21it/s]
7406418it [00:05, 1166971.26it/s]
7542445it [00:05, 1219788.92it/s]
7675739it [00:06, 1251542.46it/s]
7805775it [00:06, 1265497.81it/s]
7953437it [00:06, 1326672.00it/s]
8095898it [00:06, 1355348.02it/s]
8240506it [00:06, 1382098.45it/s]
8383578it [00:06, 1396484.27it/s]
8524267it [00:06, 1399545.71it/s]
8664679it [00:06, 1374568.14it/s]
8802549it [00:06, 1370277.76it/s]
8946061it [00:06, 1389410.57it/s]
9085231it [00:07, 1380407.38it/s]
9235013it [00:07, 1415168.50it/s]
9392422it [00:07, 1462400.36it/s]
9547203it [00:07, 1487830.62it/s]
9704019it [00:07, 1511792.77it/s]
9862095it [00:07, 1532295.63it/s]
10016328it [00:07, 1535263.72it/s]
10169906it [00:07, 1516988.41it/s]
10321688it [00:07, 1474356.08it/s]
10469411it [00:07, 1462060.65it/s]
10615812it [00:08, 1457329.76it/s]
10765699it [00:08, 1469390.58it/s]
10912753it [00:08, 1313017.94it/s]
11055983it [00:08, 1345674.80it/s]
11203022it [00:08, 1380734.84it/s]
11348039it [00:08, 1400608.63it/s]
11492481it [00:08, 1413302.67it/s]
11636035it [00:08, 1419690.45it/s]
11781243it [00:08, 1429149.71it/s]
11933871it [00:09, 1457924.03it/s]
12085990it [00:09, 1476656.71it/s]
12233961it [00:09, 1470212.32it/s]
12381200it [00:09, 1398681.50it/s]
12530880it [00:09, 1426884.16it/s]
12685492it [00:09, 1461552.89it/s]
12834171it [00:09, 1468906.85it/s]
12981495it [00:09, 1434625.54it/s]
13125401it [00:09, 1374174.11it/s]
13263549it [00:09, 1338925.83it/s]
13338540it [00:10, 1329972.88it/s]
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.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_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai
+ merge_qc -folders tih_rna_sample_00089_23H5VFLT4_s39/tih_rna_sample_00089_23H5VFLT4_s39.md -output tih_rna_sample_00089_23H5VFLT4_s39/tih_rna_sample_00089_23H5VFLT4_s39_full_basic_stats.tsv
+ head -n1 tih_rna_sample_00089_23H5VFLT4_s39/tih_rna_sample_00089_23H5VFLT4_s39_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00089_23H5VFLT4_s39/tih_rna_sample_00089_23H5VFLT4_s39_full_basic_stats.tsv