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/3c/69abbb6b9bf430c67ed76d4b5613b2/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/d2094618ff74f31543019604b2c2f5/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bam 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/90/d2094618ff74f31543019604b2c2f5/aih-tih-sc-c7b68f-R1_B23WHYVLT4_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/3c/69abbb6b9bf430c67ed76d4b5613b2/.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-c7b68f-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 fragment_size -bams aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/fragsize -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/saturation_qc.tsv samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 105489it [00:00, 1054810.53it/s] 246516it [00:00, 1263854.25it/s] 398643it [00:00, 1381333.46it/s] 560067it [00:00, 1473241.14it/s] 707392it [00:00, 1452271.86it/s] 856540it [00:00, 1465438.04it/s] 1003131it [00:00, 1452275.20it/s] 1164139it [00:00, 1501952.52it/s] 1317993it [00:00, 1513166.12it/s] 1477486it [00:01, 1538233.16it/s] 1631369it [00:01, 1381503.69it/s] 1772471it [00:01, 1372925.55it/s] 1911775it [00:01, 1331798.63it/s] 2072379it [00:01, 1409002.27it/s] 2214868it [00:01, 1354417.01it/s] 2352060it [00:01, 1359225.82it/s] 2515214it [00:01, 1437391.35it/s] 2673924it [00:01, 1480877.37it/s] 2823171it [00:01, 1484078.19it/s] 2979603it [00:02, 1507758.40it/s] 3149655it [00:02, 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[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md -output aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1.md -output aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-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-c7b68f-R1_B23WHYVLT4_1/aih-tih-sc-c7b68f-R1_B23WHYVLT4_1_full_basic_stats.tsv