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/89/fb6573e330e95d1ffeadccef739096/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/07d13f79b03bd957b435d44fa44e7e/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai 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/89/fb6573e330e95d1ffeadccef739096/.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-rnd-pltf-dev-nextflow-scratch-01/work/32/07d13f79b03bd957b435d44fa44e7e/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bam 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-a19eaa-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-a19eaa-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-a19eaa-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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-a19eaa-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-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-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-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-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai 0it [00:00, ?it/s] 157409it [00:00, 1574020.20it/s] 327352it [00:00, 1647755.58it/s] 500531it [00:00, 1686099.86it/s] 674253it [00:00, 1706215.86it/s] 849538it [00:00, 1723011.67it/s] 1024727it [00:00, 1732760.33it/s] 1198244it [00:00, 1733528.34it/s] 1372985it [00:00, 1737929.48it/s] 1552509it [00:00, 1755825.87it/s] 1731362it [00:01, 1765905.61it/s] 1908229it [00:01, 1760565.42it/s] 2084290it [00:01, 1760424.07it/s] 2262797it [00:01, 1767863.41it/s] 2439587it [00:01, 1766435.49it/s] 2616489it [00:01, 1767193.63it/s] 2793211it [00:01, 1758039.24it/s] 2970700it [00:01, 1763065.90it/s] 3152923it [00:01, 1780770.07it/s] 3331013it [00:01, 1776298.66it/s] 3508654it [00:02, 1754293.22it/s] 3687185it [00:02, 1763460.39it/s] 3865435it [00:02, 1769110.70it/s] 4042389it [00:02, 1759139.06it/s] 4218341it [00:02, 1758371.80it/s] 4394276it [00:02, 1758540.28it/s] 4570149it [00:02, 1757162.97it/s] 4745878it [00:02, 1754737.34it/s] 4921361it [00:02, 1726539.22it/s] 5095899it [00:02, 1732087.87it/s] 5271629it [00:03, 1739554.68it/s] 5448623it [00:03, 1748399.28it/s] 5624725it [00:03, 1752137.80it/s] 5799975it [00:03, 1751785.81it/s] 5975179it [00:03, 1741843.93it/s] 6149392it [00:03, 1737940.39it/s] 6324380it [00:03, 1741372.43it/s] 6503291it [00:03, 1755614.04it/s] 6678870it [00:03, 1754757.30it/s] 6854358it [00:03, 1754287.54it/s] 7029795it [00:04, 1741852.14it/s] 7204004it [00:04, 1736367.36it/s] 7381397it [00:04, 1747543.35it/s] 7556621it [00:04, 1748922.63it/s] 7731528it [00:04, 1742100.34it/s] 7905753it [00:04, 1741279.32it/s] 8080486it [00:04, 1743065.62it/s] 8254861it [00:04, 1743242.27it/s] 8429395it [00:04, 1743756.35it/s] 8603775it [00:04, 1741488.66it/s] 8777927it [00:05, 1729272.95it/s] 8955016it [00:05, 1741655.83it/s] 9130296it [00:05, 1744958.81it/s] 9304809it [00:05, 1743952.27it/s] 9482901it [00:05, 1754990.62it/s] 9658411it [00:05, 1752561.42it/s] 9838695it [00:05, 1767591.27it/s] 10015552it [00:05, 1767855.89it/s] 10192344it [00:05, 1764156.15it/s] 10368766it [00:05, 1753956.94it/s] 10545570it [00:06, 1758035.99it/s] 10722502it [00:06, 1761386.81it/s] 10898652it [00:06, 1757747.83it/s] 11074455it [00:06, 1757813.90it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai 11250243it [00:06, 1753657.38it/s] 11425615it [00:06, 1740852.30it/s] 11599722it [00:06, 1722143.83it/s] 11772572it [00:06, 1723993.90it/s] 11948489it [00:06, 1734431.33it/s] 12127526it [00:06, 1751061.21it/s] 12306154it [00:07, 1761561.46it/s] 12485127it [00:07, 1769965.88it/s] 12662147it [00:07, 1768525.66it/s] 12839016it [00:07, 1764055.36it/s] 13015435it [00:07, 1763965.34it/s] 13027719it [00:07, 1749413.80it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md -output aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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-a19eaa-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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-a19eaa-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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-a19eaa-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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-a19eaa-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.md -output aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-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-a19eaa-R1_A23WJ53LT4_1/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1_full_basic_stats.tsv