Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/553a95f294a4ad20d16e4260f2a3a4/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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/fc/3223cbb4daf5f524195181d9f58245/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/553a95f294a4ad20d16e4260f2a3a4/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/3223cbb4daf5f524195181d9f58245/.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-13a2f6-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai 142203it [00:00, 1421970.33it/s] 295235it [00:00, 1485675.99it/s] 447596it [00:00, 1502969.95it/s] 597894it [00:00, 1502226.51it/s] 751805it [00:00, 1515498.31it/s] 910068it [00:00, 1538292.20it/s] 1065623it [00:00, 1543915.68it/s] 1220016it [00:00, 1543057.64it/s] 1375188it [00:00, 1545739.48it/s] 1530248it [00:01, 1547144.35it/s] 1687984it [00:01, 1556370.52it/s] 1843622it [00:01, 1553008.87it/s] 2001348it [00:01, 1560187.37it/s] 2157370it [00:01, 1559088.60it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai 2313281it [00:01, 1554195.35it/s] 2468705it [00:01, 1548293.34it/s] 2623541it [00:01, 1541520.38it/s] 2777701it [00:01, 1534738.90it/s] 2931184it [00:01, 1533871.60it/s] 3084577it [00:02, 1522264.48it/s] 3237149it [00:02, 1523273.02it/s] 3393365it [00:02, 1534844.63it/s] 3546867it [00:02, 1531379.26it/s] 3701746it [00:02, 1536562.25it/s] 3856258it [00:02, 1539108.47it/s] 4013755it [00:02, 1549829.45it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai 4168747it [00:02, 1547734.94it/s] 4324769it [00:02, 1551462.02it/s] 4481230it [00:02, 1555388.85it/s] 4636774it [00:03, 1533772.50it/s] 4792525it [00:03, 1540806.37it/s] 4946662it [00:03, 1536940.49it/s] 5100395it [00:03, 1519025.57it/s] 5252361it [00:03, 1513693.08it/s] 5408330it [00:03, 1527314.12it/s] 5562754it [00:03, 1532201.44it/s] 5716610it [00:03, 1534079.70it/s] 5874954it [00:03, 1548778.62it/s] 5909172it [00:03, 1537601.16it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md -output aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.md -output aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_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-13a2f6-R1_B23WHYVLT4_1/aih-tih-sc-13a2f6-R1_B23WHYVLT4_1_full_basic_stats.tsv