Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/0f8be5e36f003b5dd877ca3e3052fd/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bam 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/fe/4b91ba8a5237d6b25037ce5114b74e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/0f8be5e36f003b5dd877ca3e3052fd/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai 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/fe/4b91ba8a5237d6b25037ce5114b74e/.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-00d05f-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai 156608it [00:00, 1565924.69it/s] 326330it [00:00, 1643078.95it/s] 498206it [00:00, 1677584.48it/s] 670309it [00:00, 1694584.60it/s] 842887it [00:00, 1705782.17it/s] 1013466it [00:00, 1645292.69it/s] 1186045it [00:00, 1670933.40it/s] 1353464it [00:00, 1671838.60it/s] 1524933it [00:00, 1685044.44it/s] 1698606it [00:01, 1700836.05it/s] 1870717it [00:01, 1706965.82it/s] 2044108it [00:01, 1715092.51it/s] 2215686it [00:01, 1712899.82it/s] 2387242it [00:01, 1713662.11it/s] 2565096it [00:01, 1733141.62it/s] 2739353it [00:01, 1735943.62it/s] 2913182it [00:01, 1736609.16it/s] 3087799it [00:01, 1739439.39it/s] 3261753it [00:01, 1735230.26it/s] 3435285it [00:02, 1716327.53it/s] 3606968it [00:02, 1608007.57it/s] 3769124it [00:02, 1509379.32it/s] 3921909it [00:02, 1428211.02it/s] 4066458it [00:02, 1375354.38it/s] 4205206it [00:02, 1335569.34it/s] 4339525it [00:02, 1319936.80it/s] 4506461it [00:02, 1416922.36it/s] 4667110it [00:02, 1470718.27it/s] 4815245it [00:03, 1385999.02it/s] 4955382it [00:03, 1331011.64it/s] 5089739it [00:03, 1282178.21it/s] 5218913it [00:03, 1256004.06it/s] 5345105it [00:03, 1248534.31it/s] 5485614it [00:03, 1292725.50it/s] 5629490it [00:03, 1334661.62it/s] 5776507it [00:03, 1374080.28it/s] 5935175it [00:03, 1436495.68it/s] 6099925it [00:03, 1498783.72it/s] 6271020it [00:04, 1561733.10it/s] 6431240it [00:04, 1573746.72it/s] 6588883it [00:04, 1572041.19it/s] 6758015it [00:04, 1607613.83it/s] 6918925it [00:04, 1598084.68it/s] 7078848it [00:04, 1592014.27it/s] 7239949it [00:04, 1597567.57it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai 7399767it [00:04, 1595756.01it/s] 7559385it [00:04, 1574842.84it/s] 7720012it [00:04, 1584117.00it/s] 7878494it [00:05, 1555375.39it/s] 8039647it [00:05, 1571737.15it/s] 8196953it [00:05, 1391836.03it/s] 8339893it [00:05, 1308651.63it/s] 8473928it [00:05, 1267644.87it/s] 8602827it [00:05, 1221333.92it/s] 8726424it [00:05, 1191868.52it/s] 8846519it [00:05, 1189103.03it/s] 8966040it [00:06, 1168667.53it/s] 9083280it [00:06, 1130233.91it/s] 9196632it [00:06, 1130596.68it/s] 9354105it [00:06, 1257260.01it/s] 9517567it [00:06, 1366481.34it/s] 9659058it [00:06, 1380610.75it/s] 9826533it [00:06, 1467219.06it/s] 9974488it [00:06, 1470831.60it/s] 10130886it [00:06, 1498441.57it/s] 10281076it [00:06, 1498188.75it/s] 10431137it [00:07, 1478253.06it/s] 10581363it [00:07, 1485326.59it/s] 10733782it [00:07, 1496847.72it/s] 10890256it [00:07, 1517050.25it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai 11048342it [00:07, 1536075.57it/s] 11207666it [00:07, 1553135.89it/s] 11378219it [00:07, 1598704.12it/s] 11538143it [00:07, 1577567.67it/s] 11705405it [00:07, 1605744.01it/s] 11868122it [00:07, 1611986.36it/s] 12038695it [00:08, 1639927.66it/s] 12202754it [00:08, 1636160.67it/s] 12366417it [00:08, 1634470.25it/s] 12529897it [00:08, 1613466.85it/s] 12665721it [00:08, 1503956.64it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md -output aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md -output aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_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-00d05f-R1_A23WJ53LT4_1/aih-tih-sc-00d05f-R1_A23WJ53LT4_1_full_basic_stats.tsv