Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/a8003a48e9154766d573a25cae4276/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bam 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/41/c9caa907462c4e826e0e45352c6469/.command.sh 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/41/c9caa907462c4e826e0e45352c6469/.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/b1/a8003a48e9154766d573a25cae4276/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai 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-19e09e-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai 150553it [00:00, 1505430.94it/s] 314751it [00:00, 1585697.03it/s] 473321it [00:00, 1445758.80it/s] 621143it [00:00, 1457646.17it/s] 767782it [00:00, 1454443.91it/s] 941080it [00:00, 1546502.08it/s] 1112267it [00:00, 1599510.00it/s] 1285896it [00:00, 1642474.52it/s] 1450721it [00:00, 1644221.03it/s] 1619731it [00:01, 1658267.89it/s] 1795312it [00:01, 1687965.65it/s] 1970141it [00:01, 1706145.97it/s] 2149219it [00:01, 1731699.77it/s] 2325488it [00:01, 1741019.36it/s] 2502493it [00:01, 1749731.27it/s] 2677509it [00:01, 1738230.92it/s] 2851379it [00:01, 1716219.27it/s] 3024104it [00:01, 1719459.91it/s] 3196114it [00:01, 1705843.90it/s] 3368690it [00:02, 1711372.05it/s] 3539875it [00:02, 1700708.75it/s] 3709986it [00:02, 1669637.29it/s] 3877076it [00:02, 1667181.73it/s] 4043879it [00:02, 1659030.20it/s] 4219749it [00:02, 1688477.15it/s] 4388679it [00:02, 1683413.74it/s] 4557077it [00:02, 1549788.15it/s] 4714104it [00:02, 1464610.43it/s] 4862606it [00:03, 1406660.90it/s] 5004809it [00:03, 1372106.48it/s] 5176625it [00:03, 1467165.78it/s] 5349547it [00:03, 1541003.97it/s] 5505218it [00:03, 1541687.07it/s] 5660489it [00:03, 1521291.75it/s] 5813398it [00:03, 1418669.17it/s] 5956987it [00:03, 1320270.08it/s] 6091133it [00:03, 1283593.49it/s] 6220886it [00:04, 1266112.70it/s] 6365719it [00:04, 1316398.27it/s] 6506176it [00:04, 1341314.22it/s] 6665126it [00:04, 1412711.15it/s] 6840037it [00:04, 1510692.17it/s] 7015187it [00:04, 1581374.25it/s] 7189825it [00:04, 1630133.70it/s] 7367109it [00:04, 1672410.26it/s] 7544500it [00:04, 1702603.96it/s] 7715122it [00:04, 1682831.34it/s] 7890781it [00:05, 1704654.04it/s] 8069047it [00:05, 1727822.49it/s] 8246463it [00:05, 1741498.49it/s] 8423000it [00:05, 1737490.36it/s] 8601507it [00:05, 1751622.39it/s] 8780656it [00:05, 1763485.38it/s] 8958260it [00:05, 1767203.12it/s] 9136356it [00:05, 1771289.64it/s] 9314171it [00:05, 1773312.84it/s] 9494421it [00:05, 1782022.51it/s] 9673642it [00:06, 1785040.74it/s] 9853904it [00:06, 1790282.13it/s] 10033374it [00:06, 1791576.63it/s] 10212539it [00:06, 1791501.80it/s] 10229212it [00:06, 1619554.87it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md -output aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md -output aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-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-19e09e-R1_A23WJ53LT4_1/aih-tih-sc-19e09e-R1_A23WJ53LT4_1_full_basic_stats.tsv