Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/821197f2de73600d965acec85ecc15/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bam 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/7e/1db77ac9d57601b56df3efe3056f07/.command.sh 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/7e/1db77ac9d57601b56df3efe3056f07/.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/1f/821197f2de73600d965acec85ecc15/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai 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-9fb608-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-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-9fb608-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-9fb608-R1_A23WJ53LT4_1.md.bai 150069it [00:00, 1500405.25it/s] 312933it [00:00, 1575801.51it/s] 479166it [00:00, 1615149.09it/s] 647736it [00:00, 1642868.42it/s] 819782it [00:00, 1670828.77it/s] 986866it [00:00, 1670685.52it/s] 1158123it [00:00, 1684361.78it/s] 1328703it [00:00, 1691173.80it/s] 1500957it [00:00, 1700965.30it/s] 1672849it [00:01, 1706493.45it/s] 1846029it [00:01, 1714226.25it/s] 2017452it [00:01, 1711515.62it/s] 2188605it [00:01, 1700022.35it/s] 2358625it [00:01, 1696718.67it/s] 2532551it [00:01, 1709463.36it/s] 2703513it [00:01, 1708409.00it/s] 2877258it [00:01, 1717067.97it/s] 3051857it [00:01, 1725590.25it/s] 3224425it [00:01, 1724151.97it/s] 3396847it [00:02, 1702136.72it/s] 3567126it [00:02, 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1729555.83it/s] 8749091it [00:05, 1724215.07it/s] 8922636it [00:05, 1727561.65it/s] 9095398it [00:05, 1718587.41it/s] 9271182it [00:05, 1730290.67it/s] 9444461it [00:05, 1731018.57it/s] 9617574it [00:05, 1729958.83it/s] 9790578it [00:05, 1727251.91it/s] 9963309it [00:05, 1719877.66it/s] 10135989it [00:05, 1721931.31it/s] 10308418it [00:06, 1722624.72it/s] 10481673it [00:06, 1725582.14it/s] 10654236it [00:06, 1701833.65it/s] 10824493it [00:06, 1701146.36it/s] 10994754it [00:06, 1701566.73it/s] 11166177it [00:06, 1705331.54it/s] 11339139it [00:06, 1712575.21it/s] 11510419it [00:06, 1712385.23it/s] 11683874it [00:06, 1718940.58it/s] 11858471it [00:06, 1727026.93it/s] 12034687it [00:07, 1737545.32it/s] 12208450it [00:07, 1736089.63it/s] 12382956it [00:07, 1738765.84it/s] 12556837it [00:07, 1732139.17it/s] 12730060it [00:07, 1725896.28it/s] 12902659it [00:07, 1721175.94it/s] 13077013it [00:07, 1727837.92it/s] 13251088it [00:07, 1731686.57it/s] 13424720it [00:07, 1733061.11it/s] 13598200it [00:07, 1733569.94it/s] 13771561it [00:08, 1731715.77it/s] 13945001it [00:08, 1732509.06it/s] 14118255it [00:08, 1720471.95it/s] 14290981it [00:08, 1722481.35it/s] 14463244it [00:08, 1721380.88it/s] 14635393it [00:08, 1720821.45it/s] 14809203it [00:08, 1725972.70it/s] 14981807it [00:08, 1721883.48it/s] 15156850it [00:08, 1730406.94it/s] 15329898it [00:08, 1725962.16it/s] 15504467it [00:09, 1731848.24it/s] 15678976it [00:09, 1735798.60it/s] 15853282it [00:09, 1737959.14it/s] 16027082it [00:09, 1732437.94it/s] 16202212it [00:09, 1738068.82it/s] 16376025it [00:09, 1729690.22it/s] 16549006it [00:09, 1718336.05it/s] 16685428it [00:09, 1715021.21it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md -output aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1.md -output aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-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-9fb608-R1_A23WJ53LT4_1/aih-tih-sc-9fb608-R1_A23WJ53LT4_1_full_basic_stats.tsv