Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/2b0d5a98d792d1d27f1f43056c2971/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/dc67129bd3eb97d58afeddd4934fc2/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/dc67129bd3eb97d58afeddd4934fc2/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/2b0d5a98d792d1d27f1f43056c2971/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/twist/Twist_rna_exome_AND_fusion_hg38.bed Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir aih-tih-sc-3376ed-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-3376ed-R1_B23WHYVLT4_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-3376ed-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_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-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_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-3376ed-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai 113500it [00:00, 1134671.04it/s] 257432it [00:00, 1313612.50it/s] 412862it [00:00, 1422284.20it/s] 559603it [00:00, 1440060.48it/s] 703605it [00:00, 1437938.16it/s] 866710it [00:00, 1503488.98it/s] 1029903it [00:00, 1545351.79it/s] 1194788it [00:00, 1578120.48it/s] 1362459it [00:00, 1608877.21it/s] 1527463it [00:01, 1621557.03it/s] 1693549it [00:01, 1633559.27it/s] 1861127it [00:01, 1646377.41it/s] 2025768it [00:01, 1635050.18it/s] 2189293it [00:01, 1629728.02it/s] 2355043it [00:01, 1638031.91it/s] 2521554it [00:01, 1646126.56it/s] 2686784it [00:01, 1647958.10it/s] 2853250it [00:01, 1652946.07it/s] 3024228it [00:01, 1669968.39it/s] 3191233it [00:02, 1647010.79it/s] 3358527it [00:02, 1654692.64it/s] 3524057it [00:02, 1607864.95it/s] 3691714it [00:02, 1627799.28it/s] 3854758it [00:02, 1600709.26it/s] 4015073it [00:02, 1590587.20it/s] 4174294it [00:02, 1578371.39it/s] 4337422it [00:02, 1593888.51it/s] 4496921it [00:02, 1579091.87it/s] 4654919it [00:02, 1574998.91it/s] 4813054it [00:03, 1576854.88it/s] 4975678it [00:03, 1591503.63it/s] 5134873it [00:03, 1578965.13it/s] 5292816it [00:03, 1548150.99it/s] 5452067it [00:03, 1561133.26it/s] 5610793it [00:03, 1568816.72it/s] 5768699it [00:03, 1571815.76it/s] 5927084it [00:03, 1575358.53it/s] 6085048it [00:03, 1576597.50it/s] 6245664it [00:03, 1585188.08it/s] 6414734it [00:04, 1616726.61it/s] 6578512it [00:04, 1623001.09it/s] 6740834it [00:04, 1482541.73it/s] 6898705it [00:04, 1509540.25it/s] 7051496it [00:04, 1429084.96it/s] 7215870it [00:04, 1488852.69it/s] 7374586it [00:04, 1516813.14it/s] 7539475it [00:04, 1554971.86it/s] 7704954it [00:04, 1583987.65it/s] 7870149it [00:04, 1603977.96it/s] 8035945it [00:05, 1619939.82it/s] 8203483it [00:05, 1636274.72it/s] 8367459it [00:05, 1632202.11it/s] 8530923it [00:05, 1626395.73it/s] 8696317it [00:05, 1634572.15it/s] 8864391it [00:05, 1648322.01it/s] 9032346it [00:05, 1657630.25it/s] 9199091it [00:05, 1660545.29it/s] 9365196it [00:05, 1658731.06it/s] 9532932it [00:05, 1664278.72it/s] 9699386it [00:06, 1506123.94it/s] 9864510it [00:06, 1546610.62it/s] 10027006it [00:06, 1568923.15it/s] 10185636it [00:06, 1556175.59it/s] 10346785it [00:06, 1572206.31it/s] 10510419it [00:06, 1590973.74it/s] 10670190it [00:06, 1503742.45it/s] 10837217it [00:06, 1551127.39it/s] 11003705it [00:06, 1583953.15it/s] 11164932it [00:07, 1592205.49it/s] 11324857it [00:07, 1540824.25it/s] 11488165it [00:07, 1567404.24it/s] 11655963it [00:07, 1599694.32it/s] 11820490it [00:07, 1613092.91it/s] 11982203it [00:07, 1585396.11it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai 12141104it [00:07, 1572102.44it/s] 12312947it [00:07, 1615033.00it/s] 12484123it [00:07, 1643582.36it/s] 12648715it [00:08, 1498878.14it/s] 12814023it [00:08, 1541838.12it/s] 12970313it [00:08, 1511923.67it/s] 13130382it [00:08, 1536942.17it/s] 13288292it [00:08, 1549095.44it/s] 13451908it [00:08, 1574502.06it/s] 13614472it [00:08, 1589533.85it/s] 13778056it [00:08, 1603219.83it/s] 13943210it [00:08, 1617535.01it/s] 14105236it [00:08, 1590499.35it/s] 14269080it [00:09, 1604619.35it/s] 14437657it [00:09, 1628586.97it/s] 14604556it [00:09, 1640520.98it/s] 14770263it [00:09, 1645433.80it/s] 14942810it [00:09, 1669205.23it/s] 15112499it [00:09, 1677452.10it/s] 15284886it [00:09, 1691321.38it/s] 15457196it [00:09, 1700778.37it/s] 15627306it [00:09, 1685970.28it/s] 15795954it [00:09, 1675701.48it/s] 15963567it [00:10, 1648809.40it/s] 16128553it [00:10, 1643528.34it/s] 16294008it [00:10, 1646767.70it/s] 16459178it [00:10, 1648205.59it/s] 16624037it [00:10, 1642567.50it/s] 16788322it [00:10, 1630323.86it/s] 16951916it [00:10, 1631969.41it/s] 17116079it [00:10, 1634758.31it/s] 17279574it [00:10, 1625167.76it/s] 17446417it [00:10, 1638023.42it/s] 17610245it [00:11, 1637293.34it/s] 17773992it [00:11, 1632292.71it/s] 17937235it [00:11, 1591996.82it/s] 18096699it [00:11, 1592749.06it/s] 18256373it [00:11, 1593901.02it/s] 18420116it [00:11, 1606797.02it/s] 18580884it [00:11, 1587529.75it/s] 18739739it [00:11, 1580666.12it/s] 18897875it [00:11, 1570976.78it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai 19067153it [00:11, 1606915.91it/s] 19231455it [00:12, 1617618.17it/s] 19395073it [00:12, 1623120.35it/s] 19557437it [00:12, 1609579.00it/s] 19719299it [00:12, 1612240.60it/s] 19882948it [00:12, 1619444.79it/s] 20053588it [00:12, 1645383.10it/s] 20220200it [00:12, 1651487.06it/s] 20389744it [00:12, 1664594.69it/s] 20557479it [00:12, 1668388.18it/s] 20724334it [00:12, 1649408.32it/s] 20852929it [00:13, 1598449.77it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md -output aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.depth.png [W::hts_idx_load3] The index file is older than the data file: Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi seqtool read_qc -bed Twist_rna_exome_AND_fusion_hg38.bed -n_threads 1 -bam_threads 2 aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/read_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool reads_per_target -bed Twist_rna_exome_AND_fusion_hg38.bed -threads 1 -bam_threads 2 aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/depth_stats.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool gc_bias -reference ref_genome.fa -bed Twist_rna_exome_AND_fusion_hg38.bed -bin_size 0.05 -threads 1 -bam_threads 2 aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1.md -output aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_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-3376ed-R1_B23WHYVLT4_1/aih-tih-sc-3376ed-R1_B23WHYVLT4_1_full_basic_stats.tsv