Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/1eed7f8e77b9c94b74316773428b42/aih-tih-sc-87d1a3-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/46/4bac6da06e2e1c70663bbd8cc96af5/.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/46/4bac6da06e2e1c70663bbd8cc96af5/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/1eed7f8e77b9c94b74316773428b42/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai 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-87d1a3-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai 0it [00:00, ?it/s] 141707it [00:00, 1416980.14it/s] 296052it [00:00, 1491337.51it/s] 457817it [00:00, 1548662.90it/s] 620012it [00:00, 1577560.81it/s] 780479it [00:00, 1587310.13it/s] 944380it [00:00, 1604865.06it/s] 1110639it [00:00, 1623711.94it/s] 1273011it [00:00, 1620369.91it/s] 1438940it [00:00, 1632492.98it/s] 1603767it [00:01, 1637336.33it/s] 1767672it [00:01, 1637839.41it/s] 1931458it [00:01, 1619777.23it/s] 2095513it [00:01, 1625948.67it/s] 2259605it [00:01, 1630411.69it/s] 2430682it [00:01, 1654514.44it/s] 2598078it [00:01, 1660291.06it/s] 2764129it [00:01, 1627423.84it/s] 2927026it [00:01, 1579949.31it/s] 3088776it [00:01, 1590852.35it/s] 3248142it [00:02, 1524809.36it/s] 3401289it [00:02, 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[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md -output aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.md -output aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-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-87d1a3-R1_A23WJ53LT4_1/aih-tih-sc-87d1a3-R1_A23WJ53LT4_1_full_basic_stats.tsv