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/24/88e0bb2dac689e8a60780096d45b00/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/5ebf56d5f97d636592ba51c58541d1/tih_rna_sample_00570_B23MVV7LT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/5ebf56d5f97d636592ba51c58541d1/tih_rna_sample_00570_B23MVV7LT4_1.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/24/88e0bb2dac689e8a60780096d45b00/.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 tih_rna_sample_00570_B23MVV7LT4_1 + all_qc -bam tih_rna_sample_00570_B23MVV7LT4_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 tih_rna_sample_00570_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 mkdir -p tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/full_bed.bed seqtool depth -bam tih_rna_sample_00570_B23MVV7LT4_1.md.bam -bed tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/tih_rna_sample_00570_B23MVV7LT4_1.md.depth.gz saturation_plot -bams tih_rna_sample_00570_B23MVV7LT4_1.md.bam -region chr20 -output tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00570_B23MVV7LT4_1.md.bam > tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/saturation_qc.tsv fragment_size -bams tih_rna_sample_00570_B23MVV7LT4_1.md.bam -region chr20 -output_prefix tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed tih_rna_sample_00570_B23MVV7LT4_1.md.bam > tih_rna_sample_00570_B23MVV7LT4_1.md.mpileup && contamination -input tih_rna_sample_00570_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_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: tih_rna_sample_00570_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai 140517it [00:00, 1405060.79it/s] 298968it [00:00, 1510574.25it/s] 460962it [00:00, 1560476.34it/s] 629263it [00:00, 1608821.49it/s] 792037it [00:00, 1615616.19it/s] 960162it [00:00, 1637903.66it/s] 1131315it [00:00, 1661936.00it/s] 1299966it [00:00, 1669726.46it/s] 1469000it [00:00, 1676147.07it/s] 1639243it [00:01, 1684234.08it/s] 1808851it [00:01, 1687728.14it/s] 1980010it [00:01, 1694964.96it/s] 2149507it [00:01, 1663776.07it/s] 2316610it [00:01, 1665915.50it/s] 2487533it [00:01, 1678828.42it/s] 2657125it [00:01, 1683914.19it/s] 2830033it [00:01, 1697410.86it/s] 3005627it [00:01, 1714921.24it/s] 3177596it [00:01, 1716321.39it/s] 3349255it [00:02, 1701488.55it/s] 3522750it [00:02, 1711373.34it/s] 3698370it [00:02, 1724599.18it/s] 3870864it [00:02, 1720020.20it/s] 4042891it [00:02, 1704059.19it/s] 4215589it [00:02, 1710828.11it/s] 4386710it [00:02, 1709158.58it/s] 4557652it [00:02, 1697180.61it/s] 4727510it [00:02, 1697556.32it/s] 4897288it [00:02, 1691740.44it/s] 5066479it [00:03, 1652434.65it/s] 5233983it [00:03, 1658956.46it/s] 5405829it [00:03, 1676504.27it/s] 5577640it [00:03, 1688816.08it/s] 5749960it [00:03, 1698965.12it/s] 5924289it [00:03, 1712147.42it/s] 6095567it [00:03, 1708147.14it/s] 6266427it [00:03, 1705964.74it/s] 6437055it [00:03, 1700124.47it/s] 6607092it [00:03, 1699686.66it/s] 6779891it [00:04, 1708100.35it/s] 6950716it [00:04, 1691067.48it/s] 7122606it [00:04, 1699313.13it/s] 7292577it [00:04, 1699138.46it/s] 7464879it [00:04, 1706240.66it/s] 7635526it [00:04, 1705815.94it/s] 7806683it [00:04, 1707510.43it/s] 7980396it [00:04, 1716349.70it/s] 8153160it [00:04, 1719708.60it/s] 8327571it [00:04, 1726902.28it/s] 8500839it [00:05, 1728611.49it/s] 8675501it [00:05, 1733972.36it/s] 8850594it [00:05, 1738932.83it/s] 9024490it [00:05, 1736025.56it/s] 9198096it [00:05, 1689491.81it/s] 9370496it [00:05, 1699612.80it/s] 9545491it [00:05, 1714350.61it/s] 9717364it [00:05, 1715626.38it/s] 9890570it [00:05, 1720499.40it/s] 10062707it [00:05, 1716602.01it/s] 10234589it [00:06, 1717233.94it/s] 10407473it [00:06, 1720675.50it/s] 10579572it [00:06, 1717362.71it/s] 10752612it [00:06, 1721233.80it/s] 10924753it [00:06, 1718299.79it/s] 11098414it [00:06, 1723683.44it/s] 11117330it [00:06, 1696118.10it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai tabix -s 1 -b 2 -e 2 tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/tih_rna_sample_00570_B23MVV7LT4_1.md.depth.gz seqtool depth_hist -nbins 500 tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/tih_rna_sample_00570_B23MVV7LT4_1.md.depth.gz > tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/tih_rna_sample_00570_B23MVV7LT4_1.md.depth_hist.tsv cat tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/tih_rna_sample_00570_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00570_B23MVV7LT4_1.md -output tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/tih_rna_sample_00570_B23MVV7LT4_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 tih_rna_sample_00570_B23MVV7LT4_1.md.bam > tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_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 tih_rna_sample_00570_B23MVV7LT4_1.md.bam > tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/tih_rna_sample_00570_B23MVV7LT4_1.md.depth.gz> tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_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 tih_rna_sample_00570_B23MVV7LT4_1.md.bam > tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_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: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai cat tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "tih_rna_sample_00570_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md/qc_complete.txt + merge_qc -folders tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md -output tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1_full_basic_stats.tsv