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/b0/15932e5d13cc62beea51dd86129688/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/a5bb76c766205c3e7615200f81d570/aih-tih-sc-0ce15f-R1_A23WJ53LT4_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-rnd-pltf-dev-nextflow-scratch-01/work/3f/a5bb76c766205c3e7615200f81d570/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai 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/b0/15932e5d13cc62beea51dd86129688/.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 aih-tih-sc-0ce15f-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-0ce15f-R1_A23WJ53LT4_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 aih-tih-sc-0ce15f-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/saturation_qc.tsv saturation_plot -bams aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 fragment_size -bams aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_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: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai 126732it [00:00, 1267206.40it/s] 253453it [00:00, 1085644.20it/s] 408003it [00:00, 1278060.44it/s] 538456it [00:00, 1245179.13it/s] 667511it [00:00, 1260583.91it/s] 814811it [00:00, 1330075.79it/s] 964999it [00:00, 1384783.01it/s] 1128610it [00:00, 1463351.25it/s] 1286780it [00:00, 1499865.52it/s] 1458009it [00:01, 1564861.58it/s] 1619684it [00:01, 1580609.55it/s] 1790411it [00:01, 1618942.78it/s] 1956221it [00:01, 1630725.44it/s] 2129102it [00:01, 1660244.41it/s] 2305431it [00:01, 1691217.70it/s] 2479260it [00:01, 1705332.13it/s] 2650762it [00:01, 1708110.24it/s] 2822484it [00:01, 1710741.22it/s] 2993589it [00:01, 1708978.80it/s] 3164509it [00:02, 1694534.31it/s] 3334300it [00:02, 1695508.73it/s] 3503881it [00:02, 1532134.74it/s] 3675603it [00:02, 1583567.33it/s] 3847619it [00:02, 1622346.70it/s] 4017064it [00:02, 1643074.95it/s] 4188402it [00:02, 1663553.87it/s] 4357169it [00:02, 1670579.26it/s] 4524987it [00:02, 1585545.11it/s] 4684912it [00:03, 1448913.08it/s] 4842156it [00:03, 1482390.09it/s] 5007138it [00:03, 1529044.93it/s] 5162045it [00:03, 1522410.57it/s] 5315668it [00:03, 1477052.75it/s] 5464500it [00:03, 1456211.17it/s] 5630689it [00:03, 1514850.83it/s] 5798452it [00:03, 1561980.76it/s] 5955392it [00:03, 1490249.07it/s] 6105513it [00:03, 1475729.05it/s] 6253821it [00:04, 1473383.94it/s] 6420376it [00:04, 1529092.47it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai 6589384it [00:04, 1576225.97it/s] 6760559it [00:04, 1616177.11it/s] 6922590it [00:04, 1609327.67it/s] 7087415it [00:04, 1620826.36it/s] 7169955it [00:04, 1551007.07it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md -output aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/aih-tih-sc-0ce15f-R1_A23WJ53LT4_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 aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_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 aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_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 aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_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: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md -output aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-0ce15f-R1_A23WJ53LT4_1/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1_full_basic_stats.tsv