Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/b679291e1173a9fa8c96c045dfcb12/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai 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/dc/2461c6168013c2ed2e95d0ccc8c72d/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict 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/dc/2461c6168013c2ed2e95d0ccc8c72d/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/b679291e1173a9fa8c96c045dfcb12/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bam 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-3282fd-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-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-3282fd-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-3282fd-R1_A23YTGFLT4_1.md.bai 105148it [00:00, 1002151.17it/s] 218736it [00:00, 1079174.45it/s] 360239it [00:00, 1230802.73it/s] 508466it [00:00, 1329363.91it/s] 652782it [00:00, 1370169.60it/s] 798356it [00:00, 1398955.56it/s] 938363it [00:00, 1346471.83it/s] 1073455it [00:00, 1319204.35it/s] 1209443it [00:00, 1331447.70it/s] 1342873it [00:01, 1263423.90it/s] 1469995it [00:01, 1206614.35it/s] 1591497it [00:01, 1159731.75it/s] 1708177it [00:01, 1134499.09it/s] 1822064it [00:01, 1117620.80it/s] 1934074it [00:01, 1108826.59it/s] 2045092it [00:01, 1104618.76it/s] 2155631it [00:01, 1097665.56it/s] 2265435it [00:01, 1086289.78it/s] 2374083it [00:02, 1044757.28it/s] 2484550it [00:02, 1061855.29it/s] 2592783it [00:02, 1067764.20it/s] 2713716it [00:02, 1109206.94it/s] 2847260it [00:02, 1175916.98it/s] 2991091it [00:02, 1253678.60it/s] 3138194it [00:02, 1318295.66it/s] 3275092it [00:02, 1333379.82it/s] 3408620it [00:02, 1296653.00it/s] 3550991it [00:02, 1333870.99it/s] 3689608it [00:03, 1349270.34it/s] 3829535it [00:03, 1364051.15it/s] 3966135it [00:03, 1219598.31it/s] 4091036it [00:03, 1127186.80it/s] 4206771it [00:03, 1064268.64it/s] 4315536it [00:03, 1047355.14it/s] 4423613it [00:03, 1056287.64it/s] 4559988it [00:03, 1141419.71it/s] 4697460it [00:03, 1207533.93it/s] 4828255it [00:04, 1236161.19it/s] 4961087it [00:04, 1263003.95it/s] 5106633it [00:04, 1319518.39it/s] 5259170it [00:04, 1380379.63it/s] 5405241it [00:04, 1404203.14it/s] 5546097it [00:04, 1288102.44it/s] 5677055it [00:04, 1219756.12it/s] 5801000it [00:04, 1172001.45it/s] 5919668it [00:04, 1148648.15it/s] 6035476it [00:05, 1128375.86it/s] 6148904it [00:05, 1115138.84it/s] 6260775it [00:05, 1105434.36it/s] 6374244it [00:05, 1113502.95it/s] 6485785it [00:05, 1074657.97it/s] 6593563it [00:05, 1050906.32it/s] 6698884it [00:05, 1030093.27it/s] 6802050it [00:05, 1015093.80it/s] 6903647it [00:05, 1010095.05it/s] 7004700it [00:05, 1005093.07it/s] 7105228it [00:06, 1001715.23it/s] 7205405it [00:06, 996609.93it/s] 7305829it [00:06, 998818.99it/s] 7405714it [00:06, 995161.85it/s] 7505231it [00:06, 991548.83it/s] 7604385it [00:06, 983242.91it/s] 7724971it [00:06, 1049076.13it/s] 7863221it [00:06, 1148106.97it/s] 8000500it [00:06, 1215006.78it/s] 8144386it [00:06, 1281801.44it/s] 8285647it [00:07, 1320878.52it/s] 8435295it [00:07, 1373395.21it/s] 8582255it [00:07, 1402161.10it/s] 8733371it [00:07, 1434778.58it/s] 8887950it [00:07, 1467883.59it/s] 9036179it [00:07, 1472016.73it/s] 9183408it [00:07, 1465056.04it/s] 9334388it [00:07, 1478387.15it/s] 9482250it [00:07, 1469023.64it/s] 9629180it [00:07, 1448487.91it/s] 9774102it [00:08, 1441478.87it/s] 9918299it [00:08, 1422435.70it/s] 10060610it [00:08, 1366783.97it/s] 10210684it [00:08, 1405293.83it/s] 10357567it [00:08, 1423769.62it/s] 10510879it [00:08, 1455863.17it/s] 10659551it [00:08, 1464808.42it/s] 10806278it [00:08, 1457722.51it/s] 10952224it [00:08, 1453094.38it/s] 11110767it [00:08, 1492360.94it/s] 11269778it [00:09, 1521435.13it/s] 11422030it [00:09, 1514207.47it/s] 11573531it [00:09, 1473439.00it/s] 11721149it [00:09, 1467429.47it/s] 11874905it [00:09, 1488006.56it/s] 12034231it [00:09, 1519088.39it/s] 12162132it [00:09, 1254997.41it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md -output aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1.md -output aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-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-3282fd-R1_A23YTGFLT4_1/aih-tih-sc-3282fd-R1_A23YTGFLT4_1_full_basic_stats.tsv