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/eb/7a415104a3d3232abb12e019b21fce/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/d7c4aac7f920e6eb26b49acc7fa83d/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_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/66/d7c4aac7f920e6eb26b49acc7fa83d/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_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/eb/7a415104a3d3232abb12e019b21fce/.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-f6bb6f-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 83140it [00:00, 830854.06it/s] 170783it [00:00, 857626.60it/s] 263410it [00:00, 888832.30it/s] 352294it [00:00, 875936.74it/s] 446178it [00:00, 898384.66it/s] 536056it [00:00, 893879.20it/s] 636163it [00:00, 928633.34it/s] 735817it [00:00, 950119.84it/s] 836434it [00:00, 967560.39it/s] 938796it [00:01, 984802.57it/s] 1037306it [00:01, 983270.81it/s] 1138024it [00:01, 990507.13it/s] 1237091it [00:01, 989044.81it/s] 1337254it [00:01, 992805.12it/s] 1436544it [00:01, 971154.84it/s] 1533767it [00:01, 967538.46it/s] 1632639it [00:01, 973665.02it/s] 1733457it [00:01, 983791.91it/s] 1832911it [00:01, 986927.38it/s] 1933320it [00:02, 992037.09it/s] 2033772it [00:02, 995749.48it/s] 2135827it 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8119650it [00:08, 1019738.61it/s] 8221630it [00:08, 1015259.53it/s] 8323162it [00:08, 1013104.44it/s] 8426398it [00:08, 1018825.69it/s] 8529449it [00:08, 1022295.69it/s] 8631685it [00:08, 1019846.28it/s] 8733675it [00:08, 1017140.37it/s] 8836030it [00:09, 1018926.13it/s] 8938033it [00:09, 1019237.57it/s] 9039960it [00:09, 1018776.50it/s] 9142285it [00:09, 1020099.43it/s] 9244297it [00:09, 1017624.45it/s] 9346827it [00:09, 1019905.21it/s] 9448820it [00:09, 1018898.21it/s] 9551750it [00:09, 1021995.22it/s] 9654626it [00:09, 1024004.50it/s] 9757028it [00:09, 1017706.93it/s] 9860035it [00:10, 1021381.52it/s] 9962471it [00:10, 1022252.53it/s] 10064703it [00:10, 1017624.11it/s] 10166567it [00:10, 1017907.38it/s] 10268364it [00:10, 1017681.21it/s] 10370825it [00:10, 1019615.08it/s] 10473827it [00:10, 1022712.62it/s] 10564286it [00:10, 986152.26it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md -output aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.md -output aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1/aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1_full_basic_stats.tsv