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/7f/01650cc5807de4dae8e507c897c858/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/0ebae52b4bd3f8959a02cb155256bf/aih-tih-sc-3270ab-R1_A23YTGFLT4_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/a0/0ebae52b4bd3f8959a02cb155256bf/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/01650cc5807de4dae8e507c897c858/.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-3270ab-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai 126649it [00:00, 1266427.80it/s] 275291it [00:00, 1395792.03it/s] 433033it [00:00, 1478696.63it/s] 595821it [00:00, 1537555.32it/s] 759196it [00:00, 1572217.55it/s] 922496it [00:00, 1592852.49it/s] 1088332it [00:00, 1614210.33it/s] 1251255it [00:00, 1618970.03it/s] 1414235it [00:00, 1622278.60it/s] 1579622it [00:01, 1632009.77it/s] 1744882it [00:01, 1638286.49it/s] 1909948it [00:01, 1642030.70it/s] 2081537it [00:01, 1664382.00it/s] 2247976it [00:01, 1651722.27it/s] 2413171it [00:01, 1626249.08it/s] 2579440it [00:01, 1637038.63it/s] 2745924it [00:01, 1645292.24it/s] 2910518it [00:01, 1506784.96it/s] 3069989it [00:01, 1531400.00it/s] 3234609it [00:02, 1564113.44it/s] 3400364it [00:02, 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[00:08, 1638758.48it/s] 13039767it [00:08, 1615045.12it/s] 13204266it [00:08, 1623898.61it/s] 13368340it [00:08, 1628881.00it/s] 13531364it [00:08, 1629259.00it/s] 13695504it [00:08, 1632853.20it/s] 13859402it [00:08, 1634656.12it/s] 14022899it [00:08, 1633278.09it/s] 14187285it [00:08, 1636418.60it/s] 14350943it [00:09, 1627590.86it/s] 14513723it [00:09, 1612341.33it/s] 14678595it [00:09, 1623120.21it/s] 14840947it [00:09, 1613176.65it/s] 15002866it [00:09, 1614935.82it/s] 15164386it [00:09, 1609666.45it/s] 15325372it [00:09, 1586273.84it/s] 15486882it [00:09, 1594769.62it/s] 15649075it [00:09, 1602805.86it/s] 15812240it [00:09, 1611374.56it/s] 15973422it [00:10, 1604242.67it/s] 16134590it [00:10, 1606435.15it/s] 16296681it [00:10, 1610641.44it/s] 16459303it [00:10, 1615271.90it/s] 16622185it [00:10, 1619296.99it/s] 16739092it [00:10, 1594095.86it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md -output aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.md -output aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_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-3270ab-R1_A23YTGFLT4_1/aih-tih-sc-3270ab-R1_A23YTGFLT4_1_full_basic_stats.tsv