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/4a/145b383f02fabcd3aa5aa3e30db0b2/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/35d1a9ca8699bcb7c703cbc3b2b841/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/35d1a9ca8699bcb7c703cbc3b2b841/659_bGc-T1-TRNA-1_B23WHTKLT4_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/4a/145b383f02fabcd3aa5aa3e30db0b2/.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 659_bGc-T1-TRNA-1_B23WHTKLT4_1 + all_qc -bam 659_bGc-T1-TRNA-1_B23WHTKLT4_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 659_bGc-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed seqtool depth -bam 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam -bed 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz saturation_plot -bams 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/saturation_qc.tsv fragment_size -bams 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output_prefix 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.mpileup && contamination -input 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_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: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai 0it [00:00, ?it/s] 145304it [00:00, 1452909.75it/s] 290595it [00:00, 1381456.62it/s] 462631it [00:00, 1531933.62it/s] 616377it [00:00, 1507398.69it/s] 767476it [00:00, 1487340.97it/s] 916447it [00:00, 1426735.21it/s] 1059605it [00:00, 1403309.73it/s] 1200245it [00:00, 1399236.75it/s] 1340365it [00:00, 1378826.95it/s] 1481476it [00:01, 1388429.07it/s] 1624476it [00:01, 1400828.04it/s] 1767549it [00:01, 1409742.13it/s] 1908620it [00:01, 1407715.20it/s] 2052448it [00:01, 1416775.54it/s] 2194180it [00:01, 1376287.98it/s] 2332077it [00:01, 1376020.14it/s] 2469866it [00:01, 1368762.48it/s] 2611724it [00:01, 1383448.15it/s] 2755793it [00:01, 1400402.02it/s] 2895933it [00:02, 1395602.77it/s] 3048616it [00:02, 1434630.31it/s] 3214591it [00:02, 1501770.24it/s] 3364864it [00:02, 1412180.45it/s] 3540196it [00:02, 1509801.41it/s] 3696506it [00:02, 1525237.01it/s] 3862618it [00:02, 1564965.50it/s] 4019860it [00:02, 1438405.25it/s] 4166125it [00:02, 1353147.23it/s] 4303791it [00:03, 1302894.00it/s] 4435762it [00:03, 1268580.06it/s] 4563713it [00:03, 1247223.05it/s] 4689105it [00:03, 1225862.36it/s] 4812089it [00:03, 1213411.15it/s] 4933655it [00:03, 1207592.95it/s] 5054545it [00:03, 1207008.03it/s] 5175335it [00:03, 1205367.03it/s] 5295930it [00:03, 1205195.52it/s] 5416490it [00:03, 1202265.88it/s] 5544656it [00:04, 1225659.96it/s] 5682532it [00:04, 1271125.05it/s] 5824521it [00:04, 1315425.99it/s] 5969354it [00:04, 1355025.66it/s] 6117468it [00:04, 1392707.86it/s] 6262840it [00:04, 1410815.71it/s] 6406946it [00:04, 1419836.21it/s] 6548967it [00:04, 1345741.65it/s][W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai 6684366it [00:04, 1343558.40it/s] 6825778it [00:05, 1364075.96it/s] 6962647it [00:05, 1360851.63it/s] 7104130it [00:05, 1376658.77it/s] 7244479it [00:05, 1384575.24it/s] 7388145it [00:05, 1400037.94it/s] 7535774it [00:05, 1422746.28it/s] 7684687it [00:05, 1442549.09it/s] 7829814it [00:05, 1445085.96it/s] 7979526it [00:05, 1460601.43it/s] 8127386it [00:05, 1465888.66it/s] 8274008it [00:06, 1435040.81it/s] 8368400it [00:06, 1377311.31it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz > 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv cat 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md -output 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/659_bGc-T1-TRNA-1_B23WHTKLT4_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 2 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_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 2 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz> 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_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 2 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_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: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bai cat 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bGc-T1-TRNA-1_B23WHTKLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md/qc_complete.txt + merge_qc -folders 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1.md -output 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv + head -n1 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bGc-T1-TRNA-1_B23WHTKLT4_1/659_bGc-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv