+ mkdir aih-tih-sc-3270ab-R1_A23YTGFLT4_1
+ all_qc -bam aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
126649it [00:00, 1266427.80it/s]
275291it [00:00, 1395792.03it/s]
433033it [00:00, 1478696.63it/s]
595821it [00:00, 1537555.32it/s]
759196it [00:00, 1572217.55it/s]
922496it [00:00, 1592852.49it/s]
1088332it [00:00, 1614210.33it/s]
1251255it [00:00, 1618970.03it/s]
1414235it [00:00, 1622278.60it/s]
1579622it [00:01, 1632009.77it/s]
1744882it [00:01, 1638286.49it/s]
1909948it [00:01, 1642030.70it/s]
2081537it [00:01, 1664382.00it/s]
2247976it [00:01, 1651722.27it/s]
2413171it [00:01, 1626249.08it/s]
2579440it [00:01, 1637038.63it/s]
2745924it [00:01, 1645292.24it/s]
2910518it [00:01, 1506784.96it/s]
3069989it [00:01, 1531400.00it/s]
3234609it [00:02, 1564113.44it/s]
3400364it [00:02, 1591199.52it/s]
3567371it [00:02, 1614245.66it/s]
3730291it [00:02, 1618611.39it/s]
3892718it [00:02, 1595224.01it/s]
4052693it [00:02, 1558550.88it/s]
4211860it [00:02, 1568064.26it/s]
4372216it [00:02, 1578444.38it/s]
4531584it [00:02, 1582902.50it/s]
4695761it [00:02, 1600330.57it/s]
4855946it [00:03, 1535513.98it/s]
5010128it [00:03, 1400475.07it/s]
5157909it [00:03, 1421628.99it/s]
5321990it [00:03, 1483122.80it/s]
5488794it [00:03, 1536005.02it/s]
5655752it [00:03, 1574776.03it/s]
5823466it [00:03, 1604769.14it/s]
5991162it [00:03, 1626055.84it/s]
6160725it [00:03, 1645895.71it/s]
6325792it [00:04, 1628802.52it/s]
6489037it [00:04, 1427929.80it/s]
6636445it [00:04, 1370429.15it/s]
6799509it [00:04, 1440313.21it/s]
6965048it [00:04, 1499803.83it/s]
7127686it [00:04, 1535698.45it/s]
7291353it [00:04, 1564455.69it/s]
7455191it [00:04, 1586001.20it/s]
7619561it [00:04, 1602955.35it/s]
7781625it [00:04, 1608164.88it/s]
7947169it [00:05, 1622181.65it/s]
8110709it [00:05, 1626094.23it/s]
8276073it [00:05, 1634293.54it/s]
8439721it [00:05, 1626990.20it/s]
8604579it [00:05, 1633304.92it/s]
8769281it [00:05, 1637365.78it/s]
8933919it [00:05, 1640021.79it/s]
9099743it [00:05, 1645448.42it/s]
9265209it [00:05, 1648178.96it/s]
9430584it [00:05, 1649818.39it/s]
9595623it [00:06, 1649961.92it/s]
9760634it [00:06, 1640905.05it/s]
9924746it [00:06, 1640141.50it/s]
10088775it [00:06, 1638162.54it/s]
10253282it [00:06, 1640207.59it/s]
10417311it [00:06, 1637458.53it/s]
10581286it [00:06, 1638026.54it/s]
10745093it [00:06, 1635508.90it/s]
10908648it [00:06, 1634750.69it/s]
11075682it [00:06, 1645381.31it/s]
11240224it [00:07, 1501198.77it/s]
11397894it [00:07, 1522383.07it/s]
11563709it [00:07, 1561230.01it/s]
11727850it [00:07, 1584391.61it/s]
11888564it [00:07, 1591037.59it/s]
12054484it [00:07, 1611133.98it/s]
12217699it [00:07, 1617343.33it/s]
12380368it [00:07, 1620102.31it/s]
12547428it [00:07, 1635142.26it/s]
12711176it [00:08, 1635671.14it/s]
12875784it [00:08, 1638758.48it/s]
13039767it [00:08, 1615045.12it/s]
13204266it [00:08, 1623898.61it/s]
13368340it [00:08, 1628881.00it/s]
13531364it [00:08, 1629259.00it/s]
13695504it [00:08, 1632853.20it/s]
13859402it [00:08, 1634656.12it/s]
14022899it [00:08, 1633278.09it/s]
14187285it [00:08, 1636418.60it/s]
14350943it [00:09, 1627590.86it/s]
14513723it [00:09, 1612341.33it/s]
14678595it [00:09, 1623120.21it/s]
14840947it [00:09, 1613176.65it/s]
15002866it [00:09, 1614935.82it/s]
15164386it [00:09, 1609666.45it/s]
15325372it [00:09, 1586273.84it/s]
15486882it [00:09, 1594769.62it/s]
15649075it [00:09, 1602805.86it/s]
15812240it [00:09, 1611374.56it/s]
15973422it [00:10, 1604242.67it/s]
16134590it [00:10, 1606435.15it/s]
16296681it [00:10, 1610641.44it/s]
16459303it [00:10, 1615271.90it/s]
16622185it [00:10, 1619296.99it/s]
16739092it [00:10, 1594095.86it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai
+ merge_qc -folders aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md -output aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1_full_basic_stats.tsv