+ mkdir aih-tih-sc-3b436b-R1_A23YTGFLT4_1
+ all_qc -bam aih-tih-sc-3b436b-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-3b436b-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-3b436b-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-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
0it [00:00, ?it/s]
144942it [00:00, 1449331.54it/s]
303038it [00:00, 1526713.99it/s]
466963it [00:00, 1578065.12it/s]
630349it [00:00, 1600045.55it/s]
797258it [00:00, 1624913.76it/s]
964835it [00:00, 1642066.38it/s]
1131305it [00:00, 1649438.76it/s]
1297264it [00:00, 1652633.09it/s]
1464613it [00:00, 1659126.17it/s]
1631350it [00:01, 1661644.66it/s]
1797515it [00:01, 1659314.94it/s]
1963448it [00:01, 1642468.59it/s]
2127732it [00:01, 1630949.11it/s]
2290863it [00:01, 1625316.97it/s]
2453419it [00:01, 1618661.41it/s]
2618593it [00:01, 1628429.27it/s]
2786528it [00:01, 1643607.43it/s]
2954364it [00:01, 1653975.64it/s]
3119835it [00:01, 1654169.96it/s]
3285268it [00:02, 1641286.80it/s]
3451631it [00:02, 1647915.61it/s]
3616450it [00:02, 1601507.26it/s]
3776886it [00:02, 1443342.20it/s]
3924169it [00:02, 1386840.86it/s]
4072547it [00:02, 1413184.65it/s]
4238119it [00:02, 1481033.97it/s]
4406386it [00:02, 1538593.27it/s]
4573864it [00:02, 1578012.91it/s]
4732861it [00:02, 1523391.00it/s]
4886359it [00:03, 1462698.75it/s]
5046383it [00:03, 1501468.46it/s]
5212268it [00:03, 1546648.89it/s]
5379704it [00:03, 1583773.62it/s]
5547338it [00:03, 1610921.76it/s]
5712456it [00:03, 1622780.83it/s]
5876825it [00:03, 1628962.43it/s]
6045891it [00:03, 1647301.95it/s]
6210853it [00:03, 1641989.10it/s]
6375216it [00:04, 1636496.22it/s]
6542175it [00:04, 1646325.90it/s]
6709972it [00:04, 1655731.09it/s]
6875970it [00:04, 1656964.08it/s]
6948076it [00:04, 1597117.43it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai
+ merge_qc -folders aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md -output aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1_full_basic_stats.tsv