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/92/a107a6174d6fbcc4d5ebc49422d598/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/1dae800f1299b9790681584450af62/aih-tih-sc-13d441-R1_A23YTGFLT4_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-rnd-pltf-dev-nextflow-scratch-01/work/2c/1dae800f1299b9790681584450af62/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bam 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/92/a107a6174d6fbcc4d5ebc49422d598/.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-13d441-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-13d441-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-13d441-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_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-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/full_bed.bed saturation_plot -bams aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_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-13d441-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-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-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-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-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 149655it [00:00, 1496077.03it/s] 309941it [00:00, 1558854.82it/s] 468384it [00:00, 1570508.80it/s] 636469it [00:00, 1614047.10it/s] 804849it [00:00, 1639181.61it/s] 972549it [00:00, 1652019.87it/s] 1140891it [00:00, 1662267.35it/s] 1310401it [00:00, 1672528.22it/s] 1481646it [00:00, 1684992.57it/s] 1650146it [00:01, 1680053.04it/s] 1818752it [00:01, 1681874.66it/s] 1986943it [00:01, 1672205.78it/s] 2154177it [00:01, 1671242.69it/s] 2328114it [00:01, 1691724.14it/s] 2501976it [00:01, 1705808.04it/s] 2673040it [00:01, 1707243.01it/s] 2843775it [00:01, 1699721.04it/s] 3017571it [00:01, 1711143.41it/s] 3188700it [00:01, 1705952.37it/s] 3359308it [00:02, 1693357.09it/s] 3529096it [00:02, 1694689.79it/s] 3701872it [00:02, 1704478.85it/s] 3872339it [00:02, 1690655.57it/s] 4041438it [00:02, 1689948.83it/s] 4213436it [00:02, 1698888.54it/s] 4383347it [00:02, 1693624.11it/s] 4553441it [00:02, 1695716.18it/s] 4725599it [00:02, 1703375.43it/s] 4895949it [00:02, 1694840.95it/s] 5065449it [00:03, 1667195.24it/s] 5237573it [00:03, 1683150.36it/s] 5409579it [00:03, 1693966.05it/s] 5582529it [00:03, 1704526.54it/s] 5753381it [00:03, 1705704.12it/s] 5927920it [00:03, 1717551.15it/s] 6099711it [00:03, 1714625.54it/s] 6271763it [00:03, 1716282.46it/s] 6443410it [00:03, 1697748.66it/s] 6613240it [00:03, 1692695.77it/s] 6783337it [00:04, 1695074.33it/s] 6954360it [00:04, 1699579.55it/s] 7124999it [00:04, 1701599.96it/s] 7295176it [00:04, 1696724.28it/s] 7464862it [00:04, 1695605.82it/s] 7634744it [00:04, 1696551.60it/s] 7804406it [00:04, 1690657.58it/s] 7973480it [00:04, 1687112.21it/s] 8142463it [00:04, 1687905.25it/s] 8312519it [00:04, 1691620.60it/s] 8483212it [00:05, 1696062.32it/s] 8657180it [00:05, 1709112.83it/s] 8828097it [00:05, 1700563.57it/s] 9003035it [00:05, 1715107.08it/s] 9175145it [00:05, 1716884.10it/s] 9346845it [00:05, 1710431.96it/s] 9517901it [00:05, 1705292.52it/s] 9690783it [00:05, 1712293.93it/s] 9863023it [00:05, 1715149.30it/s] 10034547it [00:05, 1714556.75it/s] 10206009it [00:06, 1709090.04it/s] 10377168it [00:06, 1709823.15it/s] 10548812it [00:06, 1711784.05it/s] 10719995it [00:06, 1711188.66it/s] 10892699it [00:06, 1715800.10it/s] 11064282it [00:06, 1708993.92it/s] 11235189it [00:06, 1702133.90it/s] 11404170it [00:06, 1693274.79it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-13d441-R1_A23YTGFLT4_1.md -output aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/aih-tih-sc-13d441-R1_A23YTGFLT4_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-13d441-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_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-13d441-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_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-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_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-13d441-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_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-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13d441-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_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-13d441-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1.md -output aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-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-13d441-R1_A23YTGFLT4_1/aih-tih-sc-13d441-R1_A23YTGFLT4_1_full_basic_stats.tsv