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/3d/1846f9527f555a6f35bf9cba541c54/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4a6b6626f8f7ea903bf3a6a42ea2fa/aih-tih-sc-3b436b-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-rnd-pltf-dev-nextflow-scratch-01/work/7b/4a6b6626f8f7ea903bf3a6a42ea2fa/aih-tih-sc-3b436b-R1_A23YTGFLT4_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/3d/1846f9527f555a6f35bf9cba541c54/.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-3b436b-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 151167it [00:00, 1511181.44it/s] 312587it [00:00, 1571707.29it/s] 478407it [00:00, 1611135.49it/s] 644196it [00:00, 1629554.43it/s] 811213it [00:00, 1644156.47it/s] 977483it [00:00, 1650418.62it/s] 1143818it [00:00, 1654611.65it/s] 1309280it [00:00, 1653094.17it/s] 1475523it [00:00, 1655979.17it/s] 1641522it [00:01, 1657060.03it/s] 1807229it [00:01, 1625867.27it/s] 1971431it [00:01, 1630685.15it/s] 2134595it [00:01, 1557581.11it/s] 2291051it [00:01, 1410744.69it/s] 2434915it [00:01, 1340263.60it/s] 2575757it [00:01, 1358588.20it/s] 2731855it [00:01, 1414781.89it/s] 2877739it [00:01, 1427269.42it/s] 3021723it [00:01, 1421415.05it/s] 3170647it [00:02, 1441010.10it/s] 3323093it [00:02, 1465456.42it/s] 3486035it [00:02, 1513838.01it/s] 3651239it [00:02, 1554742.06it/s] 3817310it [00:02, 1586253.90it/s] 3984059it [00:02, 1610317.64it/s] 4150152it [00:02, 1625335.84it/s] 4315986it [00:02, 1635177.28it/s] 4479612it [00:02, 1615415.00it/s] 4643413it [00:02, 1622094.01it/s] 4809842it [00:03, 1634630.55it/s] 4974263it [00:03, 1637423.04it/s] 5138546it [00:03, 1638958.15it/s] 5304678it [00:03, 1645609.40it/s] 5471043it [00:03, 1650975.99it/s] 5637535it [00:03, 1655121.35it/s] 5803063it [00:03, 1648149.67it/s] 5968729it [00:03, 1650661.13it/s] 6134462it [00:03, 1652625.36it/s] 6299734it [00:03, 1640917.29it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai 6464832it [00:04, 1643883.88it/s] 6631995it [00:04, 1652144.65it/s] 6797226it [00:04, 1647393.67it/s] 6948076it [00:04, 1585155.29it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md -output aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md -output aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-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-3b436b-R1_A23YTGFLT4_1/aih-tih-sc-3b436b-R1_A23YTGFLT4_1_full_basic_stats.tsv