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/c8/ec68a79be9f9b2261552dfa7fa73a7/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/eb5fa8649487c82a5d5ab7a37be9dd/659_bhK-T1-TRNA-1_B23MHV2LT4_1.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/c8/ec68a79be9f9b2261552dfa7fa73a7/.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-rnd-pltf-dev-nextflow-scratch-01/work/cc/eb5fa8649487c82a5d5ab7a37be9dd/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir 659_bhK-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bhK-T1-TRNA-1_B23MHV2LT4_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_bhK-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv saturation_plot -bams 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 fragment_size -bams 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_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_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_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_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 96401it [00:00, 933993.44it/s] 232541it [00:00, 1174810.26it/s] 358126it [00:00, 1211325.94it/s] 485581it [00:00, 1236093.55it/s] 616395it [00:00, 1261884.76it/s] 763756it [00:00, 1333596.39it/s] 904820it [00:00, 1358700.13it/s] 1040743it [00:00, 1338870.87it/s] 1175574it [00:00, 1341757.78it/s] 1309818it [00:01, 1244608.50it/s] 1435632it [00:01, 1216394.97it/s] 1558220it [00:01, 1193382.77it/s] 1678199it [00:01, 1183506.47it/s] 1796963it [00:01, 1173689.30it/s] 1914597it [00:01, 1146140.55it/s] 2029444it [00:01, 1134940.21it/s] 2180441it [00:01, 1243345.54it/s] 2332074it [00:01, 1323113.14it/s] 2464981it [00:02, 1212391.76it/s] 2588327it [00:02, 1180760.58it/s] 2707878it [00:02, 1184690.15it/s] 2835517it [00:02, 1210581.55it/s] 2957464it [00:02, 1207742.57it/s] 3078852it [00:02, 1187514.37it/s] 3198060it [00:02, 1171851.10it/s] 3315565it [00:02, 1112522.32it/s] 3427520it [00:02, 1111484.41it/s] 3543131it [00:02, 1124256.00it/s] 3659310it [00:03, 1135120.05it/s] 3807265it [00:03, 1236104.60it/s] 3931327it [00:03, 1218465.08it/s] 4059997it [00:03, 1238455.85it/s] 4199294it [00:03, 1284066.81it/s] 4327975it [00:03, 1190939.76it/s] 4448550it [00:03, 1124012.02it/s] 4562861it [00:03, 1129239.79it/s] 4690970it [00:03, 1172017.60it/s] 4819697it [00:04, 1204959.16it/s] 4975441it [00:04, 1307394.84it/s] 5121878it [00:04, 1353443.98it/s] 5263052it [00:04, 1370524.62it/s] 5405015it [00:04, 1385075.08it/s] 5543931it [00:04, 1379792.26it/s] 5683731it [00:04, 1385182.45it/s] 5834455it [00:04, 1421495.73it/s] 5980245it [00:04, 1432347.18it/s] 6123601it [00:04, 1424618.72it/s] 6266156it [00:05, 1424161.77it/s] 6408637it [00:05, 1236044.44it/s] 6536678it [00:05, 1238683.90it/s] 6667453it [00:05, 1257729.03it/s] 6807075it [00:05, 1296954.89it/s] 6958800it [00:05, 1351901.64it/s] 7105848it [00:05, 1386309.71it/s] 7245606it [00:05, 1318334.92it/s] 7379388it [00:05, 1323854.60it/s] 7512782it [00:06, 1234831.09it/s] 7637975it [00:06, 1146242.05it/s] 7754648it [00:06, 1114855.73it/s] 7871577it [00:06, 1129567.70it/s] 8007709it [00:06, 1194152.98it/s] 8148853it [00:06, 1255894.22it/s] 8280785it [00:06, 1274217.79it/s] 8417535it [00:06, 1301462.20it/s] 8548544it [00:06, 1303882.47it/s] 8683866it [00:06, 1318470.30it/s] 8816729it [00:07, 1321418.18it/s] 8962628it [00:07, 1362304.75it/s] 9101959it [00:07, 1371544.30it/s] 9239264it [00:07, 1366028.47it/s] 9375976it [00:07, 1281348.00it/s] 9514018it [00:07, 1309616.52it/s] 9653531it [00:07, 1334374.39it/s] 9787917it [00:07, 1337128.48it/s] 9922387it [00:07, 1339124.40it/s] 10056668it [00:07, 1321023.67it/s] 10202351it [00:08, 1360844.38it/s] 10338717it [00:08, 1339288.30it/s] 10478226it [00:08, 1355526.54it/s] 10614239it [00:08, 1356815.02it/s] 10750069it [00:08, 1356011.36it/s] 10887666it [00:08, 1361933.60it/s] 11034892it [00:08, 1394825.06it/s] 11181900it [00:08, 1417290.44it/s] 11323689it [00:08, 1354409.11it/s] 11462386it [00:08, 1363798.16it/s] 11605854it [00:09, 1384538.23it/s] 11746227it [00:09, 1390172.59it/s] 11885518it [00:09, 1360392.86it/s] 11928097it [00:09, 1277784.04it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/659_bhK-T1-TRNA-1_B23MHV2LT4_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_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_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_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_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_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_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_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_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_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bhK-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bhK-T1-TRNA-1_B23MHV2LT4_1/659_bhK-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv