Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/9cb008a99f76b74e458c2d2921f390/aih-tih-sc-377071-R1_A23YTGFLT4_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/c9/5ef584f1d315dafb0737450e1c1eb8/.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/c9/5ef584f1d315dafb0737450e1c1eb8/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/9cb008a99f76b74e458c2d2921f390/aih-tih-sc-377071-R1_A23YTGFLT4_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-377071-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/aih-tih-sc-377071-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-377071-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-377071-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-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-377071-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-377071-R1_A23YTGFLT4_1.md.bai 154323it [00:00, 1543135.81it/s] 318691it [00:00, 1602242.91it/s] 485736it [00:00, 1633339.61it/s] 656405it [00:00, 1662272.16it/s] 826233it [00:00, 1675233.98it/s] 996859it [00:00, 1685758.50it/s] 1165435it [00:00, 1683532.73it/s] 1336445it [00:00, 1691958.84it/s] 1507341it [00:00, 1697102.62it/s] 1677907it [00:01, 1699724.85it/s] 1847881it [00:01, 1699244.11it/s] 2017807it [00:01, 1696930.47it/s] 2187502it [00:01, 1692556.25it/s] 2359013it [00:01, 1699331.24it/s] 2529909it [00:01, 1702209.13it/s] 2700134it [00:01, 1694957.65it/s] 2873332it [00:01, 1705985.03it/s] 3049637it [00:01, 1723065.80it/s] 3221956it [00:01, 1716012.49it/s] 3393571it [00:02, 1695235.48it/s] 3563153it [00:02, 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[00:07, 1658150.99it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai 13545994it [00:08, 1646147.60it/s] 13710631it [00:08, 1645258.44it/s] 13875172it [00:08, 1636054.16it/s] 14038792it [00:08, 1623038.14it/s] 14209754it [00:08, 1648664.42it/s] 14380214it [00:08, 1665277.35it/s] 14551202it [00:08, 1678552.81it/s] 14723762it [00:08, 1692592.88it/s] 14893058it [00:08, 1690480.46it/s] 15062400it [00:08, 1691343.19it/s] 15231553it [00:09, 1687872.43it/s] 15354968it [00:09, 1678295.16it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/aih-tih-sc-377071-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/aih-tih-sc-377071-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/aih-tih-sc-377071-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/aih-tih-sc-377071-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-377071-R1_A23YTGFLT4_1.md -output aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/aih-tih-sc-377071-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-377071-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1.md -output aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1/aih-tih-sc-377071-R1_A23YTGFLT4_1_full_basic_stats.tsv