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/2c/8e8dc5afbc1e853612c5d971fed5bd/.command.sh 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/92/721bc5acfc288e83e15735b07074d7/aih-tih-sc-284856-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/2c/8e8dc5afbc1e853612c5d971fed5bd/.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/92/721bc5acfc288e83e15735b07074d7/aih-tih-sc-284856-R1_A23WJ53LT4_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 aih-tih-sc-284856-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/aih-tih-sc-284856-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-284856-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-284856-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai 0it [00:00, ?it/s] 123436it [00:00, 1233990.48it/s] 257514it [00:00, 1296766.28it/s] 394498it [00:00, 1330106.53it/s] 529790it [00:00, 1339092.83it/s] 665842it [00:00, 1346796.56it/s] 801638it [00:00, 1350452.30it/s] 937933it [00:00, 1354340.73it/s] 1073457it [00:00, 1354599.62it/s] 1208917it [00:00, 1346563.04it/s] 1344496it [00:01, 1349378.27it/s] 1480579it [00:01, 1352852.56it/s] 1615871it [00:01, 1342247.79it/s] 1751236it [00:01, 1345652.37it/s] 1887462it [00:01, 1350624.42it/s] 2023248it [00:01, 1352779.04it/s] 2159496it [00:01, 1355594.42it/s] 2295064it [00:01, 1349576.05it/s] 2430033it [00:01, 1349463.25it/s] 2565648it [00:01, 1351397.21it/s] 2700794it [00:02, 1342400.80it/s] 2837771it [00:02, 1350480.89it/s] 2975105it [00:02, 1357295.02it/s] 3111537it [00:02, 1359379.50it/s] 3247486it [00:02, 1283229.92it/s] 3376685it [00:02, 1227768.22it/s] 3512527it [00:02, 1264552.44it/s] 3648560it [00:02, 1291863.80it/s] 3785506it [00:02, 1314409.82it/s] 3919400it [00:02, 1321529.56it/s] 4054281it [00:03, 1329570.44it/s] 4188290it [00:03, 1332673.67it/s] 4324760it [00:03, 1342193.59it/s] 4461488it [00:03, 1349661.41it/s] 4596575it [00:03, 1321461.46it/s] 4728929it [00:03, 1274064.65it/s] 4857157it [00:03, 1276384.52it/s] 4985117it [00:03, 1276526.62it/s] 5112996it [00:03, 1269899.62it/s] 5246993it [00:03, 1290530.24it/s] 5250617it [00:03, 1322629.94it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/aih-tih-sc-284856-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/aih-tih-sc-284856-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/aih-tih-sc-284856-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/aih-tih-sc-284856-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-284856-R1_A23WJ53LT4_1.md -output aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/aih-tih-sc-284856-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md -output aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-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-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1_full_basic_stats.tsv