Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/3d0cf169990411532d33a9d0188fd4/GM24385_0001_RNA_0001_23H5VFLT4_s24.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/26/2239ddbe65b56864cf771415d659dc/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/3d0cf169990411532d33a9d0188fd4/GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai 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/26/2239ddbe65b56864cf771415d659dc/.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 GM24385_0001_RNA_0001_23H5VFLT4_s24 + all_qc -bam GM24385_0001_RNA_0001_23H5VFLT4_s24.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 GM24385_0001_RNA_0001_23H5VFLT4_s24 -reference ref_genome.fa -region chr20 mkdir -p GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/full_bed.bed seqtool depth -bam GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam -bed GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/GM24385_0001_RNA_0001_23H5VFLT4_s24.md.depth.gz saturation_plot -bams GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam -region chr20 -output GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/saturation_qc.tsv fragment_size -bams GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam -region chr20 -output_prefix GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s24.md.mpileup && contamination -input GM24385_0001_RNA_0001_23H5VFLT4_s24.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.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: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai 0it [00:00, ?it/s] 143913it [00:00, 1439025.01it/s][W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai 287816it [00:00, 1385346.19it/s] 426488it [00:00, 1346315.60it/s] 585827it [00:00, 1440881.30it/s] 746420it [00:00, 1499202.88it/s] 908045it [00:00, 1538418.67it/s] 1072399it [00:00, 1572422.62it/s] 1237651it [00:00, 1597712.19it/s] 1403244it [00:00, 1615406.14it/s] 1568301it [00:01, 1626177.80it/s] 1732933it [00:01, 1632263.00it/s] 1900572it [00:01, 1645618.01it/s] 2067850it [00:01, 1653780.61it/s] 2233260it [00:01, 1643638.63it/s] 2397660it [00:01, 1615595.85it/s] 2559340it [00:01, 1558654.64it/s] 2725058it [00:01, 1587166.79it/s] 2884191it [00:01, 1553694.40it/s] 3039937it [00:01, 1500592.46it/s] 3202570it [00:02, 1536510.01it/s] 3367491it [00:02, 1568664.53it/s] 3524845it [00:02, 1510304.00it/s] 3676575it [00:02, 1509982.40it/s] 3828080it [00:02, 1511407.52it/s] 3987398it [00:02, 1535314.31it/s] 4148629it [00:02, 1557890.82it/s] 4307323it [00:02, 1566300.62it/s] 4464134it [00:02, 1539401.25it/s] 4620905it [00:02, 1547690.07it/s] 4781775it [00:03, 1565655.18it/s] 4939023it [00:03, 1567643.70it/s] 5095886it [00:03, 1519327.10it/s] 5248188it [00:03, 1464841.45it/s] 5395239it [00:03, 1377820.60it/s] 5555093it [00:03, 1439129.04it/s] 5719135it [00:03, 1496295.07it/s] 5879949it [00:03, 1528552.27it/s] 6045313it [00:03, 1565043.26it/s] 6202612it [00:04, 1527364.34it/s] 6356054it [00:04, 1449047.88it/s] 6502120it [00:04, 1438158.41it/s] 6657581it [00:04, 1471367.16it/s] 6823921it [00:04, 1526948.49it/s] 6992921it [00:04, 1574627.76it/s] 7156747it [00:04, 1593335.77it/s] 7319901it [00:04, 1604601.36it/s] 7480695it [00:04, 1593590.26it/s] 7640298it [00:04, 1447112.08it/s] 7787674it [00:05, 1360276.49it/s] 7926225it [00:05, 1300055.81it/s] 8058124it [00:05, 1243640.17it/s] 8183875it [00:05, 1212611.80it/s] 8305981it [00:05, 1206783.14it/s] 8447335it [00:05, 1264204.48it/s] 8603427it [00:05, 1348484.14it/s] 8767066it [00:05, 1431572.80it/s] 8928557it [00:05, 1485069.01it/s] 9088486it [00:06, 1518656.31it/s] 9242658it [00:06, 1525445.40it/s] 9404018it [00:06, 1551605.88it/s] 9564437it [00:06, 1567232.30it/s] 9724940it [00:06, 1578474.65it/s] 9882980it [00:06, 1520166.84it/s] 10044218it [00:06, 1546992.44it/s] 10207500it [00:06, 1572179.01it/s] 10374105it [00:06, 1599894.66it/s] 10542278it [00:06, 1624083.82it/s] 10705566it [00:07, 1626663.94it/s][W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai 10872383it [00:07, 1638962.92it/s] 11036407it [00:07, 1634083.30it/s] 11199907it [00:07, 1628344.85it/s] 11338844it [00:07, 1518564.53it/s] [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai tabix -s 1 -b 2 -e 2 GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/GM24385_0001_RNA_0001_23H5VFLT4_s24.md.depth.gz seqtool depth_hist -nbins 500 GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/GM24385_0001_RNA_0001_23H5VFLT4_s24.md.depth.gz > GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/GM24385_0001_RNA_0001_23H5VFLT4_s24.md.depth_hist.tsv cat GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/GM24385_0001_RNA_0001_23H5VFLT4_s24.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title GM24385_0001_RNA_0001_23H5VFLT4_s24.md -output GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/GM24385_0001_RNA_0001_23H5VFLT4_s24.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 GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.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 GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/GM24385_0001_RNA_0001_23H5VFLT4_s24.md.depth.gz> GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.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 GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.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: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai cat GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "GM24385_0001_RNA_0001_23H5VFLT4_s24.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md/qc_complete.txt + merge_qc -folders GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md -output GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24_full_basic_stats.tsv + head -n1 GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24_full_basic_stats.tsv