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/55/4c73fd8636ea65cd3e8facc296b3e9/.command.sh 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/1a/7226bec2bf24f4fad896d51246089e/aih-tih-sc-28eb14-R1_A23YTGFLT4_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/55/4c73fd8636ea65cd3e8facc296b3e9/.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-rnd-pltf-dev-nextflow-scratch-01/work/1a/7226bec2bf24f4fad896d51246089e/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bam 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-28eb14-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 107756it [00:00, 1077427.45it/s] 228262it [00:00, 1152447.31it/s] 347050it [00:00, 1168570.30it/s] 469685it [00:00, 1191339.77it/s] 590872it [00:00, 1198709.08it/s] 712463it [00:00, 1204523.28it/s] 833876it [00:00, 1207628.37it/s] 954976it [00:00, 1208669.02it/s] 1075843it [00:00, 1173765.41it/s] 1193428it [00:01, 1160574.16it/s] 1309638it [00:01, 1146333.93it/s] 1424387it [00:01, 1142142.39it/s] 1538675it [00:01, 1130282.35it/s] 1654190it [00:01, 1137563.66it/s] 1768002it [00:01, 1134057.99it/s] 1881444it [00:01, 1095869.28it/s] 1991293it [00:01, 1096485.87it/s] 2101127it [00:01, 1089611.08it/s] 2210213it [00:01, 1060467.90it/s] 2316467it [00:02, 1041712.53it/s] 2420800it [00:02, 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1208175.73it/s] 9386669it [00:08, 1212207.99it/s] 9508976it [00:08, 1215433.03it/s] 9630523it [00:08, 1214083.42it/s] 9751934it [00:08, 1203837.16it/s] 9872338it [00:08, 1185008.75it/s] 9990907it [00:08, 1172918.24it/s] 10108256it [00:08, 1167332.07it/s] 10227424it [00:08, 1174489.88it/s] 10348290it [00:08, 1184479.81it/s] 10469246it [00:09, 1191909.20it/s] 10591175it [00:09, 1199930.19it/s] 10711196it [00:09, 1196377.11it/s] 10832130it [00:09, 1200219.42it/s] 10954906it [00:09, 1208422.52it/s] 11075763it [00:09, 1207230.14it/s] 11196496it [00:09, 1202514.86it/s] 11318684it [00:09, 1208272.05it/s] 11440372it [00:09, 1210817.28it/s] 11561462it [00:09, 1204699.48it/s] 11681944it [00:10, 1200639.08it/s] 11802339it [00:10, 1201524.26it/s] 11923980it [00:10, 1205835.69it/s] 12044571it [00:10, 1199109.32it/s] 12164494it [00:10, 1194960.88it/s] 12284813it [00:10, 1197383.68it/s] 12407586it [00:10, 1206415.86it/s] 12528376it [00:10, 1206832.44it/s] 12649435it [00:10, 1207925.52it/s] 12770233it [00:10, 1207107.81it/s] 12890972it [00:11, 1207161.64it/s] 13011928it [00:11, 1207847.86it/s] 13133037it [00:11, 1208788.07it/s] 13254235it [00:11, 1209715.15it/s] 13375717it [00:11, 1211164.88it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai 13496835it [00:11, 1208294.59it/s] 13617667it [00:11, 1205305.58it/s] 13738201it [00:11, 1203333.28it/s] 13858934it [00:11, 1204498.62it/s] 13981449it [00:11, 1210520.12it/s] 14102969it [00:12, 1211889.99it/s] 14224160it [00:12, 1210401.29it/s] 14345984it [00:12, 1212719.76it/s] 14469437it [00:12, 1219229.92it/s] 14592296it [00:12, 1222002.66it/s] 14714704it [00:12, 1222565.52it/s] 14836962it [00:12, 1207189.97it/s] 14957725it [00:12, 1205202.03it/s] 15078709it [00:12, 1206551.42it/s] 15199386it [00:12, 1200134.28it/s] 15319420it [00:13, 1200041.68it/s] 15439948it [00:13, 1201576.86it/s] 15505077it [00:13, 1176147.85it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md -output aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.md -output aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1/aih-tih-sc-28eb14-R1_A23YTGFLT4_1_full_basic_stats.tsv