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/96/e71d9fb85948e6b445e43318c7a29a/.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/f8/f11bfeefe0f762c2fe42dc131a621d/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/e71d9fb85948e6b445e43318c7a29a/.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-rnd-pltf-dev-nextflow-scratch-01/work/f8/f11bfeefe0f762c2fe42dc131a621d/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir aih-tih-sc-d113b5-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/full_bed.bed saturation_plot -bams aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 fragment_size -bams aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/fragsize -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/saturation_qc.tsv seqtool depth -bam aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.depth.gz samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-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-d113b5-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-d113b5-R1_B23WHYVLT4_1.md.bai 113433it [00:00, 1134252.66it/s] 247696it [00:00, 1256782.53it/s] 378542it [00:00, 1280343.08it/s] 513473it [00:00, 1307537.93it/s] 644227it [00:00, 1244530.85it/s] 782763it [00:00, 1290838.53it/s] 933495it [00:00, 1360025.01it/s] 1075560it [00:00, 1378970.57it/s] 1213814it [00:00, 1369364.80it/s] 1358715it [00:01, 1393620.59it/s] 1498282it [00:01, 1390799.47it/s] 1649943it [00:01, 1428747.39it/s] 1797503it [00:01, 1442838.14it/s] 1941884it [00:01, 1432148.40it/s] 2089695it [00:01, 1445858.99it/s] 2234727it [00:01, 1447088.24it/s] 2379485it [00:01, 1432866.83it/s] 2530239it [00:01, 1455055.89it/s] 2675809it [00:01, 1452935.97it/s] 2822148it [00:02, 1456033.73it/s] 2967785it [00:02, 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1565878.77it/s] 7217379it [00:05, 1543768.99it/s] 7376479it [00:05, 1557627.91it/s] 7532332it [00:05, 1528610.73it/s] 7694525it [00:05, 1556002.13it/s] 7850293it [00:05, 1461246.10it/s] 7997618it [00:05, 1367215.79it/s] 8136074it [00:05, 1312945.60it/s] 8268686it [00:06, 1273324.79it/s] 8396899it [00:06, 1241054.44it/s] 8521550it [00:06, 1186679.03it/s] 8640746it [00:06, 1184653.56it/s] 8762627it [00:06, 1194200.28it/s] 8882361it [00:06, 1192362.71it/s] 9001809it [00:06, 1188692.45it/s] 9124648it [00:06, 1200202.30it/s] 9244797it [00:06, 1194006.69it/s] 9364813it [00:06, 1195772.19it/s] 9484454it [00:07, 1191433.01it/s] 9603641it [00:07, 1175057.48it/s] 9721211it [00:07, 1159911.48it/s] 9837267it [00:07, 1143574.48it/s] 9988785it [00:07, 1252210.61it/s] 10147357it [00:07, 1350462.74it/s] 10297071it [00:07, 1393891.72it/s] 10450874it [00:07, 1436728.54it/s] 10594821it [00:07, 1434851.60it/s] 10746245it [00:07, 1458501.04it/s] 10903127it [00:08, 1491409.47it/s] 11052384it [00:08, 1481171.53it/s] 11200597it [00:08, 1467289.76it/s] 11348597it [00:08, 1470973.89it/s] 11495760it [00:08, 1364638.00it/s] 11633748it [00:08, 1363227.13it/s] 11779720it [00:08, 1390885.12it/s] 11932513it [00:08, 1430695.85it/s] 12088440it [00:08, 1468393.79it/s] 12235879it [00:08, 1464702.77it/s] 12356186it [00:09, 1359934.87it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md -output aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1.md -output aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-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-d113b5-R1_B23WHYVLT4_1/aih-tih-sc-d113b5-R1_B23WHYVLT4_1_full_basic_stats.tsv