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/89/7002f298f6710fc24a65522ad3f8bf/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/e28d19736965fa68181081548e70f1/tih_rna_sample_00161_B23WHTKLT4_2.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/e28d19736965fa68181081548e70f1/tih_rna_sample_00161_B23WHTKLT4_2.md.bam 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/89/7002f298f6710fc24a65522ad3f8bf/.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_00161_B23WHTKLT4_2 + all_qc -bam tih_rna_sample_00161_B23WHTKLT4_2.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_00161_B23WHTKLT4_2 -reference ref_genome.fa -region chr20 mkdir -p tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.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_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/full_bed.bed saturation_plot -bams tih_rna_sample_00161_B23WHTKLT4_2.md.bam -region chr20 -output tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/saturation_plot.png -threads 1 seqtool depth -bam tih_rna_sample_00161_B23WHTKLT4_2.md.bam -bed tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/tih_rna_sample_00161_B23WHTKLT4_2.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00161_B23WHTKLT4_2.md.bam > tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/saturation_qc.tsv fragment_size -bams tih_rna_sample_00161_B23WHTKLT4_2.md.bam -region chr20 -output_prefix tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.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_00161_B23WHTKLT4_2.md.bam > tih_rna_sample_00161_B23WHTKLT4_2.md.mpileup && contamination -input tih_rna_sample_00161_B23WHTKLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.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_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.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_00161_B23WHTKLT4_2.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai 108013it [00:00, 1080056.35it/s] 220918it [00:00, 1108837.08it/s] 334503it [00:00, 1121142.52it/s] 448340it [00:00, 1127918.44it/s] 562731it [00:00, 1133596.60it/s] 676091it [00:00, 1133077.37it/s] 789399it [00:00, 1128620.99it/s] 902676it [00:00, 1129887.01it/s] 1016734it [00:00, 1133204.75it/s] 1130113it [00:01, 1133364.68it/s] 1243452it [00:01, 1130806.69it/s] 1356668it [00:01, 1131194.04it/s] 1470874it [00:01, 1134462.78it/s] 1585017it [00:01, 1136544.73it/s] 1699645it [00:01, 1139390.49it/s] 1814534it [00:01, 1142229.58it/s] 1928758it [00:01, 1140382.88it/s] 2042822it [00:01, 1140436.70it/s] 2156867it [00:01, 1140214.27it/s] 2271024it [00:02, 1140601.71it/s] 2385085it [00:02, 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12286208it [00:11, 1091947.07it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai 12402053it [00:11, 1111825.42it/s] 12513250it [00:11, 1103105.39it/s] 12624059it [00:11, 1104565.67it/s] 12734534it [00:11, 1092031.23it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai 12843777it [00:11, 1088377.22it/s] 12952641it [00:11, 1083943.49it/s] 13061054it [00:11, 1077593.19it/s] 13169095it [00:11, 1078407.64it/s] 13283833it [00:11, 1098918.13it/s] 13396263it [00:12, 1106416.50it/s] 13509747it [00:12, 1114889.43it/s] 13621255it [00:12, 1104742.56it/s] 13731761it [00:12, 1087637.57it/s] 13840594it [00:12, 1082848.88it/s] 13952333it [00:12, 1093036.79it/s] 14064081it [00:12, 1100271.58it/s] 14178623it [00:12, 1113648.57it/s] 14291834it [00:12, 1119139.90it/s] 14404837it [00:12, 1122372.78it/s] 14517097it [00:13, 1119873.39it/s] 14629101it [00:13, 1070419.20it/s] 14741193it [00:13, 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17976076it [00:16, 1134272.21it/s] 18089558it [00:16, 1125649.37it/s] 18203832it [00:16, 1130707.99it/s] 18317742it [00:16, 1133192.49it/s] 18432199it [00:16, 1136567.49it/s] 18545878it [00:16, 1132937.59it/s] 18659189it [00:16, 1131489.49it/s] 18773314it [00:16, 1134313.07it/s] 18846867it [00:16, 1108877.44it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai tabix -s 1 -b 2 -e 2 tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/tih_rna_sample_00161_B23WHTKLT4_2.md.depth.gz seqtool depth_hist -nbins 500 tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/tih_rna_sample_00161_B23WHTKLT4_2.md.depth.gz > tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/tih_rna_sample_00161_B23WHTKLT4_2.md.depth_hist.tsv cat tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/tih_rna_sample_00161_B23WHTKLT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00161_B23WHTKLT4_2.md -output tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/tih_rna_sample_00161_B23WHTKLT4_2.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_00161_B23WHTKLT4_2.md.bam > tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.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_00161_B23WHTKLT4_2.md.bam > tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.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_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/tih_rna_sample_00161_B23WHTKLT4_2.md.depth.gz> tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.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_00161_B23WHTKLT4_2.md.bam > tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.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_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00161_B23WHTKLT4_2.md.bai cat tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "tih_rna_sample_00161_B23WHTKLT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md/qc_complete.txt + merge_qc -folders tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2.md -output tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2_full_basic_stats.tsv + head -n1 tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00161_B23WHTKLT4_2/tih_rna_sample_00161_B23WHTKLT4_2_full_basic_stats.tsv