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/f2/2af1616bffaf15f202027a8a43f3d5/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/1a955ab9a8c8bff22827236c8ccd0e/aih-tih-sc-ced210-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/64/1a955ab9a8c8bff22827236c8ccd0e/aih-tih-sc-ced210-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/f2/2af1616bffaf15f202027a8a43f3d5/.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-ced210-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-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-ced210-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-ced210-R1_A23WJ53LT4_1.md.bai 142546it [00:00, 1425366.21it/s] 302100it [00:00, 1525434.49it/s] 469243it [00:00, 1592077.28it/s] 638055it [00:00, 1629973.65it/s] 805722it [00:00, 1646784.57it/s] 974996it [00:00, 1662393.41it/s] 1145415it [00:00, 1676044.84it/s] 1317254it [00:00, 1689374.44it/s] 1488955it [00:00, 1698000.93it/s] 1658756it [00:01, 1696293.81it/s] 1828618it [00:01, 1696992.10it/s] 1998318it [00:01, 1681260.60it/s] 2169101it [00:01, 1689240.27it/s] 2345716it [00:01, 1712345.21it/s] 2516982it [00:01, 1712339.70it/s] 2688238it [00:01, 1710785.94it/s] 2860944it [00:01, 1715648.98it/s] 3032521it [00:01, 1715599.88it/s] 3204090it [00:01, 1705461.69it/s] 3374655it [00:02, 1693257.80it/s] 3544961it [00:02, 1696096.08it/s] 3718637it [00:02, 1708091.08it/s] 3890030it [00:02, 1709824.06it/s] 4061029it [00:02, 1706421.27it/s] 4232610it [00:02, 1709214.24it/s] 4403541it [00:02, 1702290.54it/s] 4574678it [00:02, 1704988.01it/s] 4747690it [00:02, 1712489.56it/s] 4918948it [00:02, 1703108.34it/s] 5089275it [00:03, 1697817.34it/s] 5262050it [00:03, 1706731.77it/s] 5434676it [00:03, 1712436.83it/s] 5607709it [00:03, 1717694.87it/s] 5781330it [00:03, 1723226.96it/s] 5954392it [00:03, 1725428.48it/s] 6128000it [00:03, 1728608.70it/s] 6300866it [00:03, 1727230.83it/s] 6474080it [00:03, 1728690.13it/s] 6647254it [00:03, 1729457.79it/s] 6820202it [00:04, 1727232.65it/s] 6992928it [00:04, 1724664.10it/s] 7165397it [00:04, 1722013.47it/s] 7337601it [00:04, 1719762.90it/s] 7509894it [00:04, 1720697.51it/s] 7681965it [00:04, 1711096.28it/s] 7853087it [00:04, 1705815.09it/s] 8025774it [00:04, 1712083.08it/s] 8197560it [00:04, 1713788.80it/s] 8371507it [00:04, 1721461.68it/s] 8546554it [00:05, 1730136.00it/s] 8721517it [00:05, 1735866.06it/s] 8897342it [00:05, 1742561.08it/s] 9071603it [00:05, 1739809.46it/s] 9245589it [00:05, 1735825.09it/s] 9419176it [00:05, 1730009.60it/s] 9592183it [00:05, 1726975.40it/s] 9765425it [00:05, 1728588.82it/s] 9938967it [00:05, 1730620.24it/s] 10112033it [00:05, 1727375.21it/s] 10284774it [00:06, 1724980.73it/s] 10457697it [00:06, 1726237.51it/s] 10630323it [00:06, 1725854.22it/s] 10802910it [00:06, 1720132.77it/s] 10976514it [00:06, 1724879.18it/s] 11149019it [00:06, 1724918.48it/s] 11321515it [00:06, 1720225.74it/s] 11493543it [00:06, 1717373.32it/s] 11667411it [00:06, 1723702.71it/s] 11840102it [00:06, 1724572.06it/s] 12012910it [00:07, 1725613.30it/s] 12079838it [00:07, 1710085.46it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-ced210-R1_A23WJ53LT4_1.md -output aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ced210-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1.md -output aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-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-ced210-R1_A23WJ53LT4_1/aih-tih-sc-ced210-R1_A23WJ53LT4_1_full_basic_stats.tsv