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/e2/af607422ac7ebe54163753b280676a/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/384ac91142ab464d2552a33424a1e1/aih-tih-sc-01c779-R1_A23YTGFLT4_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-rnd-pltf-dev-nextflow-scratch-01/work/56/384ac91142ab464d2552a33424a1e1/aih-tih-sc-01c779-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/e2/af607422ac7ebe54163753b280676a/.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-01c779-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 97114it [00:00, 971071.47it/s] 200770it [00:00, 1009556.77it/s] 301726it [00:00, 1006700.51it/s] 404572it [00:00, 1015184.80it/s] 509291it [00:00, 1026688.29it/s] 613084it [00:00, 1030484.44it/s] 716837it [00:00, 1032763.53it/s] 821515it [00:00, 1037204.62it/s] 925820it [00:00, 1039012.42it/s] 1029929it [00:01, 1039632.57it/s] 1134005it [00:01, 1039846.62it/s] 1238213it [00:01, 1040508.10it/s] 1342281it [00:01, 1040540.18it/s] 1446336it [00:01, 1036001.92it/s] 1552368it [00:01, 1043290.78it/s] 1656703it [00:01, 1043255.83it/s] 1761914it [00:01, 1045858.22it/s] 1867772it [00:01, 1049659.64it/s] 1973262it [00:01, 1051211.51it/s] 2078386it [00:02, 1050428.29it/s] 2183431it [00:02, 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1050813.30it/s] 5354955it [00:05, 1052851.68it/s] 5461982it [00:05, 1058053.11it/s] 5567792it [00:05, 1056243.95it/s] 5673420it [00:05, 1054920.50it/s] 5778915it [00:05, 1052774.00it/s] 5884195it [00:05, 1052545.64it/s] 5989452it [00:05, 1050177.42it/s] 6095696it [00:05, 1053828.40it/s] 6201467it [00:05, 1054968.77it/s] 6306966it [00:06, 1052017.62it/s] 6412171it [00:06, 1049695.27it/s] 6517143it [00:06, 1048884.50it/s] 6622034it [00:06, 1046073.06it/s] 6726644it [00:06, 1045667.26it/s] 6831212it [00:06, 1045526.00it/s] 6935766it [00:06, 1041248.28it/s] 7040822it [00:06, 1044012.50it/s] 7145812it [00:06, 1045757.83it/s] 7250664it [00:06, 1046567.02it/s] 7355324it [00:07, 1044228.91it/s] 7459750it [00:07, 1043725.52it/s] 7565193it [00:07, 1046911.39it/s] 7670432it [00:07, 1048533.99it/s] 7776319it [00:07, 1051612.88it/s] 7881482it [00:07, 1049028.73it/s] 7987298it [00:07, 1051741.92it/s] 8093202it [00:07, 1053911.57it/s] 8198828it [00:07, 1054507.11it/s] 8304281it [00:07, 1052963.40it/s] 8409579it [00:08, 1052303.65it/s] 8514811it [00:08, 1048989.57it/s] 8619893it [00:08, 1049518.47it/s] 8724847it [00:08, 1047278.02it/s] 8829577it [00:08, 1046404.50it/s] 8934414it [00:08, 1046974.13it/s] 9039113it [00:08, 1045822.76it/s] 9143697it [00:08, 1045196.38it/s] 9248218it [00:08, 1044669.02it/s] 9352686it [00:08, 1043026.69it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai 9456990it [00:09, 1021575.49it/s] 9559242it [00:09, 1020622.75it/s] 9661369it [00:09, 1006890.68it/s] 9762820it [00:09, 1009116.31it/s] 9866486it [00:09, 1017173.19it/s] 9971394it [00:09, 1026643.19it/s] 10075811it [00:09, 1031846.92it/s] 10181626it [00:09, 1039682.95it/s] 10287314it [00:09, 1044806.05it/s] 10394007it [00:09, 1051411.58it/s] 10499164it [00:10, 1050006.12it/s] 10604176it [00:10, 1046354.72it/s] 10710088it [00:10, 1050151.71it/s] 10816284it [00:10, 1053665.98it/s] 10922130it [00:10, 1055084.38it/s] 11027644it [00:10, 1054373.83it/s] 11133085it [00:10, 1050822.98it/s] 11238173it [00:10, 1048122.21it/s] 11342990it [00:10, 1043914.17it/s] 11447745it [00:10, 1044979.63it/s] 11552399it [00:11, 1045330.72it/s] 11657209it [00:11, 1046139.99it/s] 11762417it [00:11, 1047901.43it/s] 11867290it [00:11, 1048133.47it/s] 11972105it [00:11, 1016936.02it/s] 12074000it [00:11, 974082.41it/s] 12175316it [00:11, 985257.22it/s] 12277323it [00:11, 995347.43it/s] 12382636it [00:11, 1012152.98it/s] 12488332it [00:11, 1025325.19it/s] 12593157it [00:12, 1032091.82it/s] 12697147it [00:12, 1034382.77it/s] 12801473it [00:12, 1037010.54it/s] 12906816it [00:12, 1041898.55it/s] 13011215it [00:12, 1042503.71it/s] 13115503it [00:12, 1032324.12it/s] 13218783it [00:12, 1017040.98it/s] 13322650it [00:12, 1023408.37it/s] 13379510it [00:12, 1041975.28it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-01c779-R1_A23YTGFLT4_1.md -output aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-01c779-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1.md -output aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-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-01c779-R1_A23YTGFLT4_1/aih-tih-sc-01c779-R1_A23YTGFLT4_1_full_basic_stats.tsv