Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/ff9613254c9acad79c3268187a01a5/659_bKP-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.fa Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/429204c83667ac36a68ee412d25504/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/ff9613254c9acad79c3268187a01a5/659_bKP-T1-TRNA-1_B23MHV2LT4_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/56/429204c83667ac36a68ee412d25504/.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_bKP-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 132943it [00:00, 1329317.17it/s] 268906it [00:00, 1345303.21it/s] 403435it [00:00, 1330310.94it/s] 536484it [00:00, 1282059.84it/s] 680808it [00:00, 1338511.75it/s] 826455it [00:00, 1377841.76it/s] 974456it [00:00, 1410799.22it/s] 1121642it [00:00, 1430045.50it/s] 1264822it [00:00, 1272668.38it/s] 1415584it [00:01, 1339160.29it/s] 1564141it [00:01, 1381299.95it/s] 1711732it [00:01, 1408852.90it/s] 1862120it [00:01, 1436679.11it/s] 2007018it [00:01, 1374336.00it/s] 2145803it [00:01, 1313964.43it/s] 2278504it [00:01, 1306463.28it/s] 2414570it [00:01, 1321883.85it/s] 2547457it [00:01, 1277801.20it/s] 2675916it [00:02, 1240331.05it/s] 2800507it [00:02, 1174191.70it/s] 2918766it [00:02, 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1503182.23it/s] 7100467it [00:05, 1453315.83it/s] 7246184it [00:05, 1394160.54it/s] 7386276it [00:05, 1365753.40it/s] 7538665it [00:05, 1410906.69it/s] 7689356it [00:05, 1438708.18it/s] 7836275it [00:05, 1447607.60it/s] 7986403it [00:05, 1463416.74it/s] 8133030it [00:06, 1416777.90it/s] 8284331it [00:06, 1444718.74it/s] 8433836it [00:06, 1459452.99it/s] 8581647it [00:06, 1464939.74it/s] 8729287it [00:06, 1468314.63it/s] 8876291it [00:06, 1460997.70it/s] 9022515it [00:06, 1425053.81it/s] 9165276it [00:06, 1424383.64it/s] 9315128it [00:06, 1446212.99it/s] 9459913it [00:07, 1398211.26it/s] 9600147it [00:07, 1318933.46it/s] 9749873it [00:07, 1369031.63it/s] 9902386it [00:07, 1413725.28it/s] 10054526it [00:07, 1444971.89it/s] 10204933it [00:07, 1462277.87it/s] 10351741it [00:07, 1447467.54it/s] 10500585it [00:07, 1459502.32it/s] 10650196it [00:07, 1470314.37it/s] 10803359it [00:07, 1488513.10it/s] 10957227it [00:08, 1503437.74it/s] 11109346it [00:08, 1508712.06it/s] 11262159it [00:08, 1514493.85it/s] 11413680it [00:08, 1506196.08it/s] 11568252it [00:08, 1517962.91it/s] 11722621it [00:08, 1525555.64it/s] 11878433it [00:08, 1535269.71it/s] 12031989it [00:08, 1353549.62it/s] 12180455it [00:08, 1389429.67it/s] 12334859it [00:09, 1432880.77it/s] 12487590it [00:09, 1459915.02it/s] 12642385it [00:09, 1485461.13it/s] 12795910it [00:09, 1499893.82it/s] 12951166it [00:09, 1515272.07it/s] 13106668it [00:09, 1527038.75it/s] 13139385it [00:09, 1379252.87it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bKP-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-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_bKP-T1-TRNA-1_B23MHV2LT4_1/659_bKP-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv