Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/6f6202a1c2bee4019e4192cc380993/659_b4x-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.fa Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/ca318f4a77f5bfc72c827961063111/.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/d1/ca318f4a77f5bfc72c827961063111/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/6f6202a1c2bee4019e4192cc380993/659_b4x-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.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_b4x-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed saturation_plot -bams 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 97514it [00:00, 974957.30it/s] 203520it [00:00, 1024958.37it/s] 310817it [00:00, 1046825.68it/s] 418769it [00:00, 1059685.59it/s] 525814it [00:00, 1063531.73it/s] 633229it [00:00, 1067104.84it/s] 741803it [00:00, 1073160.21it/s] 851125it [00:00, 1079510.93it/s] 961240it [00:00, 1086239.85it/s] 1070248it [00:01, 1087266.37it/s] 1178975it [00:01, 1085565.79it/s] 1287821it [00:01, 1086408.51it/s] 1397978it [00:01, 1090962.41it/s] 1507075it [00:01, 1089001.73it/s] 1615977it [00:01, 1088937.23it/s] 1725799it [00:01, 1091669.54it/s] 1834967it [00:01, 1089932.82it/s] 1943967it [00:01, 1089805.20it/s] 2052949it [00:01, 1088614.17it/s] 2161812it [00:02, 1071942.73it/s][W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai 2270669it [00:02, 1076837.08it/s] 2378398it [00:02, 1071253.40it/s] 2486894it [00:02, 1075294.51it/s] 2594451it [00:02, 1070448.18it/s] 2701517it [00:02, 1069511.94it/s] 2810095it [00:02, 1074331.40it/s] 2918886it [00:02, 1078326.24it/s] 3027985it [00:02, 1082080.06it/s] 3107120it [00:02, 1077148.10it/s] [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md -output 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1.md -output 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-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_b4x-T1-TRNA-1_B23MHV2LT4_1/659_b4x-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv