Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/d9338f7dfa370cdbe9db25b61f5708/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.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/ca9d93929da6471310f2e763f807ff/.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/ca9d93929da6471310f2e763f807ff/.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/9d/d9338f7dfa370cdbe9db25b61f5708/1173_C31_T1_RNA_SLD_01_A23T55JLT4_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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1 + all_qc -bam 1173_C31_T1_RNA_SLD_01_A23T55JLT4_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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed seqtool depth -bam 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -bed 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz saturation_plot -bams 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -region chr20 -output 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_qc.tsv fragment_size -bams 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -region chr20 -output_prefix 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup && contamination -input 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_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: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 0it [00:00, ?it/s] 125592it [00:00, 1255828.38it/s][W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 261745it [00:00, 1317969.56it/s] 399703it [00:00, 1346074.06it/s] 534311it [00:00, 1337230.01it/s] 672522it [00:00, 1353201.23it/s] 810904it [00:00, 1363563.49it/s] 951480it [00:00, 1377309.68it/s] 1089615it [00:00, 1378504.76it/s] 1227473it [00:00, 1362680.49it/s] 1365739it [00:01, 1368741.77it/s] 1502648it [00:01, 1208160.72it/s] 1626811it [00:01, 1077836.34it/s] 1738946it [00:01, 1009603.07it/s] 1843173it [00:01, 975757.59it/s] 1942848it [00:01, 936617.61it/s] 2037865it [00:01, 910381.13it/s] 2148144it [00:01, 961452.08it/s] 2277750it [00:01, 1053350.11it/s] 2417052it [00:02, 1149130.61it/s] 2555644it [00:02, 1216984.98it/s] 2694691it [00:02, 1267428.06it/s] 2832348it [00:02, 1299449.88it/s] 2973265it [00:02, 1331832.45it/s] 3112289it [00:02, 1349136.78it/s] 3251412it [00:02, 1361652.02it/s] 3393384it [00:02, 1378957.40it/s] 3534861it [00:02, 1389625.09it/s] 3675834it [00:02, 1395623.26it/s] 3815535it [00:03, 1395429.21it/s] 3955470it [00:03, 1396567.07it/s] 4095195it [00:03, 1371206.20it/s] 4232465it [00:03, 1362514.11it/s] 4372264it [00:03, 1372968.77it/s] 4481830it [00:03, 1257989.18it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai tabix -s 1 -b 2 -e 2 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz seqtool depth_hist -nbins 500 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv cat 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz> 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_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: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bai cat 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md/qc_complete.txt + merge_qc -folders 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv + head -n1 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1/1173_C31_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv