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/ce/ea0686309417ad545f412df63a99ae/.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/6f/6f68937af1ee9ca5c19c3c0f4d07c0/aih-tih-sc-20b7e4-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/ce/ea0686309417ad545f412df63a99ae/.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/6f/6f68937af1ee9ca5c19c3c0f4d07c0/aih-tih-sc-20b7e4-R1_B23WHYVLT4_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-20b7e4-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-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-20b7e4-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-20b7e4-R1_B23WHYVLT4_1.md.bai 66971it [00:00, 669635.60it/s] 139118it [00:00, 700101.86it/s] 210446it [00:00, 706097.80it/s] 281528it [00:00, 707946.26it/s] 353659it [00:00, 712748.21it/s] 426724it [00:00, 718819.07it/s] 499371it [00:00, 721304.71it/s] 572325it [00:00, 723912.80it/s] 644991it [00:00, 724756.67it/s] 717637it [00:01, 725253.36it/s] 791823it [00:01, 730322.44it/s] 865054it [00:01, 730912.41it/s] 938146it [00:01, 729667.04it/s] 1011114it [00:01, 727291.54it/s] 1083845it [00:01, 718913.48it/s] 1155757it [00:01, 716214.46it/s] 1229368it [00:01, 722048.95it/s] 1303073it [00:01, 726510.70it/s] 1376226it [00:01, 727998.01it/s] 1449037it [00:02, 724089.10it/s] 1521829it [00:02, 725215.56it/s] 1594359it [00:02, 724534.89it/s] 1666819it [00:02, 721343.68it/s] 1740168it [00:02, 724896.97it/s] 1812664it [00:02, 719638.86it/s] 1885417it [00:02, 721973.44it/s] 1958480it [00:02, 724533.57it/s] 2031238it [00:02, 725429.67it/s] 2105007it [00:02, 729083.31it/s] 2177921it [00:03, 728221.93it/s] 2250794it [00:03, 728361.75it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai 2324021it [00:03, 729518.55it/s] 2396975it [00:03, 726696.57it/s] 2469649it [00:03, 717760.98it/s] 2541450it [00:03, 713942.08it/s] 2612863it [00:03, 713426.55it/s] 2686032it [00:03, 718771.57it/s] 2759153it [00:03, 722468.43it/s] 2831692it [00:03, 723326.88it/s] 2904117it [00:04, 723560.35it/s] 2976479it [00:04, 721215.30it/s] 3048606it [00:04, 717994.00it/s] 3120762it [00:04, 719043.47it/s] 3192672it [00:04, 715484.78it/s] 3266101it [00:04, 721076.90it/s] 3339033it [00:04, 723526.12it/s] 3412653it [00:04, 727291.65it/s] 3486494it [00:04, 730607.43it/s] 3560166it [00:04, 732422.84it/s] 3633412it [00:05, 732227.02it/s] 3706638it [00:05, 729260.60it/s] 3798684it [00:05, 786337.87it/s] 3903597it [00:05, 864954.02it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai 3998311it [00:05, 889549.79it/s] 4092652it [00:05, 905668.77it/s] 4200301it [00:05, 956847.10it/s] 4308028it [00:05, 992932.31it/s] 4409799it [00:05, 1000243.72it/s] 4514804it [00:05, 1015160.16it/s] 4607331it [00:06, 764999.26it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md -output aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md -output aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-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-20b7e4-R1_B23WHYVLT4_1/aih-tih-sc-20b7e4-R1_B23WHYVLT4_1_full_basic_stats.tsv