Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/a9839ff2ecf956bbb10e00001b0519/tih_rna_sample_00592_B23MVV7LT4_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/c7/a5af02e5bb6cd5fdef94ba45ec5964/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/a9839ff2ecf956bbb10e00001b0519/tih_rna_sample_00592_B23MVV7LT4_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/c7/a5af02e5bb6cd5fdef94ba45ec5964/.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 tih_rna_sample_00592_B23MVV7LT4_1 + all_qc -bam tih_rna_sample_00592_B23MVV7LT4_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 tih_rna_sample_00592_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 mkdir -p tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/full_bed.bed seqtool depth -bam tih_rna_sample_00592_B23MVV7LT4_1.md.bam -bed tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/tih_rna_sample_00592_B23MVV7LT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00592_B23MVV7LT4_1.md.bam > tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/saturation_qc.tsv saturation_plot -bams tih_rna_sample_00592_B23MVV7LT4_1.md.bam -region chr20 -output tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/saturation_plot.png -threads 1 fragment_size -bams tih_rna_sample_00592_B23MVV7LT4_1.md.bam -region chr20 -output_prefix tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed tih_rna_sample_00592_B23MVV7LT4_1.md.bam > tih_rna_sample_00592_B23MVV7LT4_1.md.mpileup && contamination -input tih_rna_sample_00592_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_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: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s] 135599it [00:00, 1355564.68it/s] 280235it [00:00, 1408809.54it/s] 430039it [00:00, 1449524.10it/s] 576905it [00:00, 1457058.04it/s] 723358it [00:00, 1459731.47it/s] 872374it [00:00, 1470056.87it/s] 1019380it [00:00, 1457447.01it/s] 1167469it [00:00, 1464819.07it/s] 1313971it [00:00, 1438247.62it/s] 1457902it [00:01, 1213769.52it/s] 1585009it [00:01, 1202087.80it/s] 1709105it [00:01, 1181475.54it/s] 1829865it [00:01, 1160587.80it/s] 1947668it [00:01, 1151983.60it/s] 2072793it [00:01, 1179887.89it/s] 2191797it [00:01, 1177324.19it/s] 2315331it [00:01, 1194102.78it/s] 2436336it [00:01, 1198744.80it/s] 2556610it [00:02, 1191682.66it/s] 2687580it [00:02, 1226438.29it/s] 2810481it [00:02, 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6385646it [00:05, 1095783.30it/s] 6495467it [00:05, 1096032.00it/s] 6615321it [00:05, 1126231.87it/s] 6737072it [00:05, 1153263.69it/s] 6852552it [00:05, 1127654.01it/s] 6965534it [00:05, 1117967.85it/s] 7078059it [00:06, 1120084.88it/s] 7190178it [00:06, 1111059.28it/s] 7301366it [00:06, 1069690.06it/s] 7411069it [00:06, 1077563.49it/s] 7521370it [00:06, 1084973.29it/s] 7635983it [00:06, 1102950.84it/s] 7751121it [00:06, 1117259.99it/s] 7862992it [00:06, 1106088.14it/s] 7973719it [00:06, 1103600.05it/s] 8084823it [00:06, 1105680.72it/s] 8199486it [00:07, 1117840.64it/s] 8311321it [00:07, 1099536.48it/s] 8421369it [00:07, 1081077.84it/s] 8529587it [00:07, 1066205.46it/s] 8646597it [00:07, 1096524.80it/s] 8756395it [00:07, 1095329.35it/s] 8866028it [00:07, 1070264.03it/s] 8973222it [00:07, 995102.12it/s] 9104135it [00:07, 1082855.62it/s] 9239773it [00:08, 1160848.96it/s] 9369501it [00:08, 1200245.36it/s] 9490818it [00:08, 1203943.60it/s] 9622040it [00:08, 1235839.40it/s] 9747801it [00:08, 1242155.66it/s] 9877927it [00:08, 1259714.39it/s] 10004213it [00:08, 1259113.12it/s] 10130344it [00:08, 1229899.54it/s] 10186320it [00:08, 1158468.86it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai tabix -s 1 -b 2 -e 2 tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/tih_rna_sample_00592_B23MVV7LT4_1.md.depth.gz seqtool depth_hist -nbins 500 tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/tih_rna_sample_00592_B23MVV7LT4_1.md.depth.gz > tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/tih_rna_sample_00592_B23MVV7LT4_1.md.depth_hist.tsv cat tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/tih_rna_sample_00592_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00592_B23MVV7LT4_1.md -output tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/tih_rna_sample_00592_B23MVV7LT4_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 tih_rna_sample_00592_B23MVV7LT4_1.md.bam > tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_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 tih_rna_sample_00592_B23MVV7LT4_1.md.bam > tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/tih_rna_sample_00592_B23MVV7LT4_1.md.depth.gz> tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_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 tih_rna_sample_00592_B23MVV7LT4_1.md.bam > tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_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: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai cat tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "tih_rna_sample_00592_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md/qc_complete.txt + merge_qc -folders tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md -output tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1_full_basic_stats.tsv