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/95/089d8e425d2e679e84a3468aa2d287/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/69093f62d2c71e4122cbef7c98d724/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_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/ac/69093f62d2c71e4122cbef7c98d724/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_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/95/089d8e425d2e679e84a3468aa2d287/.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-d2f1f4-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_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-d2f1f4-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 134234it [00:00, 1342248.48it/s] 280988it [00:00, 1415910.37it/s] 429721it [00:00, 1448493.36it/s] 575946it [00:00, 1453897.35it/s] 722593it [00:00, 1458401.41it/s] 870007it [00:00, 1463732.66it/s] 1017613it [00:00, 1467739.07it/s] 1166291it [00:00, 1473779.79it/s] 1313669it [00:00, 1453111.99it/s] 1459042it [00:01, 1411022.01it/s] 1606175it [00:01, 1428961.64it/s] 1754591it [00:01, 1445414.21it/s] 1906852it [00:01, 1468469.22it/s] 2054482it [00:01, 1470792.85it/s] 2207795it [00:01, 1489439.05it/s] 2360774it [00:01, 1501510.95it/s] 2513754it [00:01, 1509973.11it/s] 2665883it [00:01, 1513193.36it/s] 2818291it [00:01, 1516439.62it/s] 2969962it [00:02, 1516298.89it/s] 3121611it [00:02, 1510079.29it/s] 3272870it [00:02, 1510811.16it/s] 3423965it [00:02, 1500091.83it/s] 3573999it [00:02, 1493725.65it/s] 3723391it [00:02, 1483371.48it/s] 3872958it [00:02, 1486928.02it/s] 4021670it [00:02, 1481131.57it/s] 4169798it [00:02, 1477166.41it/s] 4319485it [00:02, 1483014.35it/s] 4467798it [00:03, 1478542.26it/s] 4616221it [00:03, 1480162.35it/s] 4766364it [00:03, 1486436.61it/s] 4917070it [00:03, 1492506.11it/s] 5066328it [00:03, 1470493.37it/s] 5214427it [00:03, 1473586.79it/s] 5365036it [00:03, 1483238.17it/s] 5518369it [00:03, 1498155.96it/s] 5670836it [00:03, 1506058.62it/s] 5824638it [00:03, 1515599.24it/s] 5977208it [00:04, 1518569.54it/s] 6129084it [00:04, 1512680.58it/s] 6280370it [00:04, 1493591.31it/s] 6429790it [00:04, 1490743.07it/s] 6578923it [00:04, 1490897.83it/s] 6728472it [00:04, 1492247.62it/s] 6877718it [00:04, 1488658.42it/s] 7026599it [00:04, 1487831.59it/s] 7176510it [00:04, 1491175.73it/s] 7325636it [00:04, 1485362.54it/s] 7474182it [00:05, 1477987.73it/s] 7622376it [00:05, 1479143.74it/s] 7770300it [00:05, 1469519.62it/s] 7917269it [00:05, 1465872.87it/s] 8063867it [00:05, 1462758.21it/s] 8210150it [00:05, 1457887.66it/s] 8355945it [00:05, 1453500.50it/s] 8502178it [00:05, 1456025.72it/s] 8650577it [00:05, 1464350.83it/s] 8798475it [00:05, 1468700.59it/s] 8945352it [00:06, 1414074.64it/s] 9090178it [00:06, 1423959.97it/s] 9232904it [00:06, 1402869.59it/s] 9382118it [00:06, 1474183.23it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md -output aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.md -output aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-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-d2f1f4-R1_B23WHYVLT4_1/aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1_full_basic_stats.tsv