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/dd/719d24c024e7b45c209f6f2df1769b/.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/f6/3d35294eddb9d8263a6f683c7ee9dd/aih-tih-sc-1274d4-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/dd/719d24c024e7b45c209f6f2df1769b/.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/f6/3d35294eddb9d8263a6f683c7ee9dd/aih-tih-sc-1274d4-R1_A23YTGFLT4_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-1274d4-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai 111178it [00:00, 1111645.89it/s] 225353it [00:00, 1129315.93it/s] 340285it [00:00, 1138413.12it/s] 456959it [00:00, 1149566.95it/s] 574380it [00:00, 1158424.52it/s] 690829it [00:00, 1160460.73it/s] 806876it [00:00, 1142105.28it/s] 921145it [00:00, 1127885.30it/s] 1033996it [00:00, 1124338.01it/s] 1146470it [00:01, 1119000.68it/s] 1259974it [00:01, 1123821.28it/s] 1372381it [00:01, 1120652.67it/s] 1484463it [00:01, 1115807.09it/s] 1600629it [00:01, 1129514.14it/s] 1716190it [00:01, 1137309.15it/s] 1833373it [00:01, 1147634.59it/s] 1948155it [00:01, 1141631.99it/s] 2062571it [00:01, 1142361.48it/s] 2180865it [00:01, 1154477.01it/s] 2296327it [00:02, 1149975.35it/s] 2411367it [00:02, 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1149294.09it/s] 9106762it [00:08, 1151574.18it/s] 9225387it [00:08, 1161795.76it/s] 9343376it [00:08, 1167170.19it/s] 9461489it [00:08, 1171320.25it/s] 9580499it [00:08, 1176915.52it/s] 9698209it [00:08, 1176625.12it/s] 9817677it [00:08, 1182012.01it/s] 9936200it [00:09, 1182956.25it/s] 10054503it [00:09, 1182617.83it/s] 10172770it [00:09, 1181349.69it/s] 10291435it [00:09, 1182905.87it/s] 10409729it [00:09, 1180317.87it/s] 10528301it [00:09, 1181915.86it/s] 10648930it [00:09, 1189196.65it/s] 10767853it [00:09, 1184247.12it/s] 10886406it [00:09, 1184611.48it/s] 11004872it [00:09, 1181243.76it/s] 11123001it [00:10, 1175924.85it/s] 11240601it [00:10, 1173466.84it/s] 11357953it [00:10, 1169280.56it/s] 11475776it [00:10, 1171928.53it/s] 11592974it [00:10, 1171683.11it/s] 11710336it [00:10, 1172166.49it/s] 11827706it [00:10, 1172603.19it/s] 11944969it [00:10, 1171056.23it/s] 12063583it [00:10, 1175448.00it/s] 12181130it [00:10, 1168463.84it/s] 12300701it [00:11, 1176575.01it/s] 12418370it [00:11, 1166177.74it/s] 12535013it [00:11, 1165483.81it/s] 12651992it [00:11, 1166747.53it/s] 12769190it [00:11, 1168288.65it/s] 12887560it [00:11, 1172880.48it/s] 13004857it [00:11, 1170540.37it/s] 13124129it [00:11, 1177150.92it/s] 13242449it [00:11, 1178936.02it/s] 13360348it [00:11, 1173456.58it/s] 13480316it [00:12, 1181271.41it/s] 13600563it [00:12, 1187591.66it/s] 13719331it [00:12, 1186845.06it/s] 13838022it [00:12, 1185384.00it/s] 13956565it [00:12, 1184317.96it/s] 14075000it [00:12, 1179658.74it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai 14192972it [00:12, 1177362.31it/s] 14310713it [00:12, 1163730.52it/s] 14427119it [00:12, 1147490.40it/s] 14543848it [00:12, 1153306.87it/s] 14660614it [00:13, 1157512.87it/s] 14777481it [00:13, 1160723.96it/s] 14896086it [00:13, 1168252.35it/s] 15014513it [00:13, 1173016.88it/s] 15131836it [00:13, 1170063.24it/s] 15249569it [00:13, 1172210.75it/s] 15366802it [00:13, 1171691.00it/s] 15483980it [00:13, 1165864.96it/s] 15600578it [00:13, 1165360.59it/s] 15717122it [00:13, 1162026.66it/s] 15833331it [00:14, 1158771.12it/s] 15949214it [00:14, 1154695.35it/s] 16064689it [00:14, 1149350.03it/s] 16181239it [00:14, 1154136.49it/s] 16297552it [00:14, 1156675.65it/s] 16415038it [00:14, 1162089.71it/s] 16532567it [00:14, 1165952.96it/s] 16651071it [00:14, 1171647.39it/s] 16769674it [00:14, 1175935.60it/s] 16887272it [00:14, 1171528.37it/s] 17006857it [00:15, 1178780.85it/s] 17124742it [00:15, 1178368.83it/s] 17244582it [00:15, 1184345.17it/s] 17363021it [00:15, 1183402.90it/s] 17483029it [00:15, 1188258.83it/s] 17602651it [00:15, 1190625.25it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai 17721716it [00:15, 1179858.33it/s] 17839725it [00:15, 1173802.85it/s] 17958310it [00:15, 1177359.13it/s] 18076351it [00:15, 1178244.97it/s] 18194698it [00:16, 1179786.91it/s] 18312686it [00:16, 1177131.33it/s] 18430589it [00:16, 1177679.88it/s] 18548769it [00:16, 1178890.36it/s] 18578339it [00:16, 1131633.36it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md -output aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md -output aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1_full_basic_stats.tsv