+ mkdir aih-tih-sc-9f6030-R1_A23WJ53LT4_1
+ all_qc -bam aih-tih-sc-9f6030-R1_A23WJ53LT4_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-9f6030-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_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-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_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-9f6030-R1_A23WJ53LT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
114011it [00:00, 1140048.57it/s]
228016it [00:00, 1120237.45it/s]
340064it [00:00, 1086653.31it/s]
461723it [00:00, 1136691.52it/s]
576248it [00:00, 1139710.71it/s]
690373it [00:00, 1140194.26it/s]
804474it [00:00, 1128873.88it/s]
917432it [00:00, 1123280.84it/s]
1043538it [00:00, 1165834.56it/s]
1161372it [00:01, 1169644.79it/s]
1282446it [00:01, 1182134.47it/s]
1400709it [00:01, 1165117.84it/s]
1530371it [00:01, 1204420.55it/s]
1650922it [00:01, 1198883.02it/s]
1789495it [00:01, 1254639.93it/s]
1930830it [00:01, 1302038.47it/s]
2061142it [00:01, 1250980.60it/s]
2194244it [00:01, 1274259.26it/s]
2322084it [00:01, 1189879.94it/s]
2442371it [00:02, 1192872.90it/s]
2578254it [00:02, 1240414.30it/s]
2703171it [00:02, 1231587.98it/s]
2826933it [00:02, 1222999.91it/s]
2949648it [00:02, 1210253.54it/s]
3070964it [00:02, 1193837.68it/s]
3190563it [00:02, 1133541.79it/s]
3308803it [00:02, 1147331.24it/s]
3436109it [00:02, 1183414.62it/s]
3560790it [00:02, 1201876.49it/s]
3681402it [00:03, 1138395.27it/s]
3796150it [00:03, 1116812.88it/s]
3919912it [00:03, 1151166.33it/s]
4035659it [00:03, 1151802.71it/s]
4173024it [00:03, 1216541.33it/s]
4295166it [00:03, 1201174.34it/s]
4418426it [00:03, 1210368.76it/s]
4551471it [00:03, 1245793.37it/s]
4676301it [00:03, 1234339.34it/s]
4799924it [00:04, 1189259.29it/s]
4927854it [00:04, 1215272.07it/s]
5049784it [00:04, 1200084.54it/s]
5185190it [00:04, 1244959.20it/s]
5321409it [00:04, 1279337.35it/s]
5455924it [00:04, 1298683.30it/s]
5586028it [00:04, 1247206.08it/s]
5714572it [00:04, 1258253.14it/s]
5840834it [00:04, 1251268.26it/s]
5972029it [00:04, 1269046.61it/s]
6104788it [00:05, 1286313.43it/s]
6233621it [00:05, 1233539.05it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
6360555it [00:05, 1243861.98it/s]
6493046it [00:05, 1267466.80it/s]
6624686it [00:05, 1281854.64it/s]
6753155it [00:05, 1280303.96it/s]
6881383it [00:05, 1275192.27it/s]
7009040it [00:05, 1265628.84it/s]
7136839it [00:05, 1269266.77it/s]
7263844it [00:05, 1240473.75it/s]
7388069it [00:06, 1236151.94it/s]
7511803it [00:06, 1222390.48it/s]
7647028it [00:06, 1260362.50it/s]
7777725it [00:06, 1274116.67it/s]
7905260it [00:06, 1257913.44it/s]
8038583it [00:06, 1280116.53it/s]
8179429it [00:06, 1318151.79it/s]
8319123it [00:06, 1341573.28it/s]
8453390it [00:06, 1310046.66it/s]
8584621it [00:07, 1303553.56it/s]
8715130it [00:07, 1250214.15it/s]
8852545it [00:07, 1285726.92it/s]
8984283it [00:07, 1294806.33it/s]
9128005it [00:07, 1336608.80it/s]
9267129it [00:07, 1352737.37it/s]
9408781it [00:07, 1371649.73it/s]
9548481it [00:07, 1379122.79it/s]
9687129it [00:07, 1381295.27it/s]
9825367it [00:07, 1284785.82it/s]
9955254it [00:08, 1273517.12it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
10083564it [00:08, 1222156.53it/s]
10214319it [00:08, 1246168.98it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
10339752it [00:08, 1211615.91it/s]
10471909it [00:08, 1242829.29it/s]
10596824it [00:08, 1198909.12it/s]
10724174it [00:08, 1220005.10it/s]
10852467it [00:08, 1238167.33it/s]
10996262it [00:08, 1296521.65it/s]
11127095it [00:08, 1299612.44it/s]
11271580it [00:09, 1342589.75it/s]
11406138it [00:09, 1325071.90it/s]
11538894it [00:09, 1240006.25it/s]
11616248it [00:09, 1238518.72it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_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-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md.bai
+ merge_qc -folders aih-tih-sc-9f6030-R1_A23WJ53LT4_1/aih-tih-sc-9f6030-R1_A23WJ53LT4_1.md -output aih-tih-sc-9f6030-R1_A23WJ53LT4_1/aih-tih-sc-9f6030-R1_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-9f6030-R1_A23WJ53LT4_1/aih-tih-sc-9f6030-R1_A23WJ53LT4_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-9f6030-R1_A23WJ53LT4_1/aih-tih-sc-9f6030-R1_A23WJ53LT4_1_full_basic_stats.tsv