+ mkdir aih-tih-sc-693ffe-R1_A23WJ53LT4_1
+ all_qc -bam aih-tih-sc-693ffe-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-693ffe-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-693ffe-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-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-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-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
0it [00:00, ?it/s]
144790it [00:00, 1446356.50it/s]
297057it [00:00, 1491190.29it/s]
460595it [00:00, 1556809.39it/s]
630164it [00:00, 1611592.42it/s]
802279it [00:00, 1651066.90it/s]
975130it [00:00, 1677367.89it/s]
1147915it [00:00, 1693755.88it/s]
1320077it [00:00, 1702596.34it/s]
1493771it [00:00, 1713306.74it/s]
1665653it [00:01, 1714983.94it/s]
1841476it [00:01, 1728197.77it/s]
2015028it [00:01, 1730398.05it/s]
2189634it [00:01, 1735121.59it/s]
2367377it [00:01, 1747865.54it/s]
2542164it [00:01, 1741971.19it/s]
2717133it [00:01, 1744263.28it/s]
2892554it [00:01, 1747194.70it/s]
3067277it [00:01, 1746787.07it/s]
3241958it [00:01, 1740962.24it/s]
3416060it [00:02, 1722964.04it/s]
3588398it [00:02, 1722026.11it/s]
3760629it [00:02, 1702422.61it/s]
3930929it [00:02, 1564437.77it/s]
4089492it [00:02, 1533699.93it/s]
4258079it [00:02, 1576411.32it/s]
4429975it [00:02, 1617195.04it/s]
4603462it [00:02, 1651331.75it/s]
4769788it [00:02, 1654797.75it/s]
4938889it [00:02, 1665451.74it/s]
5105894it [00:03, 1556975.67it/s]
5271287it [00:03, 1584441.56it/s]
5449124it [00:03, 1640326.99it/s]
5627598it [00:03, 1682432.64it/s]
5803607it [00:03, 1705250.42it/s]
5979803it [00:03, 1721983.60it/s]
6155709it [00:03, 1732977.17it/s]
6331320it [00:03, 1739844.30it/s]
6505568it [00:03, 1739210.47it/s]
6679673it [00:03, 1728316.62it/s]
6856323it [00:04, 1739663.15it/s]
7030862it [00:04, 1741334.40it/s]
7205132it [00:04, 1741721.99it/s]
7379358it [00:04, 1730175.66it/s]
7556041it [00:04, 1741081.16it/s]
7732925it [00:04, 1749351.33it/s]
7908978it [00:04, 1752469.77it/s]
8085764it [00:04, 1757057.74it/s]
8263868it [00:04, 1764220.92it/s]
8440305it [00:04, 1763784.74it/s]
8616694it [00:05, 1760040.17it/s]
8792707it [00:05, 1747097.61it/s]
8967442it [00:05, 1716813.14it/s]
9141869it [00:05, 1724887.23it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
9318197it [00:05, 1736245.19it/s]
9491903it [00:05, 1718814.72it/s]
9663868it [00:05, 1700738.12it/s]
9835916it [00:05, 1706480.16it/s]
10007741it [00:05, 1709897.78it/s]
10180919it [00:05, 1716379.58it/s]
10355504it [00:06, 1725146.63it/s]
10529423it [00:06, 1729318.33it/s]
10704414it [00:06, 1735457.58it/s]
10880901it [00:06, 1744244.10it/s]
11059131it [00:06, 1755626.35it/s]
11235151it [00:06, 1756978.74it/s]
11410858it [00:06, 1750974.34it/s]
11586593it [00:06, 1752865.74it/s]
11718301it [00:06, 1705762.61it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-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-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md.bai
+ merge_qc -folders aih-tih-sc-693ffe-R1_A23WJ53LT4_1/aih-tih-sc-693ffe-R1_A23WJ53LT4_1.md -output aih-tih-sc-693ffe-R1_A23WJ53LT4_1/aih-tih-sc-693ffe-R1_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-693ffe-R1_A23WJ53LT4_1/aih-tih-sc-693ffe-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-693ffe-R1_A23WJ53LT4_1/aih-tih-sc-693ffe-R1_A23WJ53LT4_1_full_basic_stats.tsv