Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/c3f2ed9e43605873828aaedf9434ad/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 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/78/e33ff3e859c1963d92600cc984edc8/.command.sh 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/78/e33ff3e859c1963d92600cc984edc8/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/c3f2ed9e43605873828aaedf9434ad/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam 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 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2 + all_qc -bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_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 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2 -reference ref_genome.fa -region chr20 mkdir -p 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/full_bed.bed seqtool depth -bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -bed 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz saturation_plot -bams 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -region chr20 -output 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/saturation_qc.tsv fragment_size -bams 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -region chr20 -output_prefix 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.mpileup && contamination -input 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_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: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 123890it [00:00, 1232451.40it/s] 261485it [00:00, 1316615.28it/s] 402978it [00:00, 1361405.88it/s] 539134it [00:00, 1292860.60it/s] 669994it [00:00, 1298300.37it/s] 837628it [00:00, 1423939.37it/s] 1003354it [00:00, 1499028.20it/s] 1170334it [00:00, 1552791.48it/s] 1325980it [00:00, 1551206.63it/s] 1496377it [00:01, 1598041.08it/s] 1660028it [00:01, 1609726.91it/s] 1826301it [00:01, 1625712.35it/s] 1988979it [00:01, 1623864.59it/s] 2159732it [00:01, 1649035.64it/s] 2324694it [00:01, 1647102.64it/s] 2493669it [00:01, 1659871.53it/s] 2665434it [00:01, 1677184.22it/s] 2836073it [00:01, 1685894.79it/s] 3005906it [00:01, 1689594.62it/s] 3174879it [00:02, 1405815.66it/s] 3340559it [00:02, 1471658.26it/s] 3501826it [00:02, 1510122.12it/s] 3657784it [00:02, 1506056.14it/s] 3811836it [00:02, 1507252.95it/s] 3964979it [00:02, 1467017.02it/s] 4123035it [00:02, 1499208.85it/s] 4274402it [00:02, 1492595.22it/s] 4443170it [00:02, 1549265.91it/s] 4598977it [00:03, 1536811.27it/s] 4767387it [00:03, 1579852.44it/s] 4935399it [00:03, 1609361.69it/s] 5109103it [00:03, 1647206.71it/s] 5282942it [00:03, 1674215.46it/s] 5453039it [00:03, 1682164.38it/s] 5625736it [00:03, 1695516.75it/s] 5797106it [00:03, 1700915.99it/s] 5967293it [00:03, 1679520.19it/s] 6135370it [00:03, 1676931.18it/s] 6303149it [00:04, 1542234.39it/s] 6459487it [00:04, 1506392.67it/s] 6624647it [00:04, 1547055.43it/s] 6785596it [00:04, 1564899.18it/s] 6952613it [00:04, 1595262.03it/s] 7115896it [00:04, 1606088.84it/s] 7283100it [00:04, 1625491.02it/s] 7446093it [00:04, 1521090.42it/s] 7599803it [00:04, 1342043.10it/s] 7738512it [00:05, 1314942.94it/s] 7900016it [00:05, 1395113.22it/s] 7916309it [00:05, 1539147.90it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai tabix -s 1 -b 2 -e 2 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz seqtool depth_hist -nbins 500 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.depth_hist.tsv cat 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_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 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_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 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz> 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_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 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_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: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bai cat 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md/qc_complete.txt + merge_qc -folders 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv + head -n1 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv