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/9f/6bb2c8bb9f76fc27e02b62c6f493f7/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/708d33eb0ba367a6094ae2c52d245c/659_cIX-T1-TRNA-1_B23WHTKLT4_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/69/708d33eb0ba367a6094ae2c52d245c/659_cIX-T1-TRNA-1_B23WHTKLT4_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/9f/6bb2c8bb9f76fc27e02b62c6f493f7/.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 659_cIX-T1-TRNA-1_B23WHTKLT4_1 + all_qc -bam 659_cIX-T1-TRNA-1_B23WHTKLT4_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 659_cIX-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed seqtool depth -bam 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam -bed 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz saturation_plot -bams 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/saturation_qc.tsv fragment_size -bams 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output_prefix 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.mpileup && contamination -input 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_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: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai 138601it [00:00, 1385479.50it/s] 294977it [00:00, 1490303.34it/s] 456597it [00:00, 1547755.18it/s] 623030it [00:00, 1593744.98it/s] 790149it [00:00, 1621584.76it/s] 955172it [00:00, 1631298.86it/s] 1122616it [00:00, 1645378.04it/s] 1287155it [00:00, 1615287.47it/s] 1448798it [00:00, 1520260.70it/s] 1615292it [00:01, 1562662.35it/s] 1780763it [00:01, 1589817.90it/s] 1943952it [00:01, 1602273.79it/s] 2110765it [00:01, 1621852.59it/s] 2275230it [00:01, 1628634.74it/s] 2442891it [00:01, 1642946.09it/s] 2607415it [00:01, 1641965.04it/s] 2776265it [00:01, 1655827.92it/s] 2944750it [00:01, 1664495.01it/s] 3111286it [00:01, 1660834.91it/s] 3277431it [00:02, 1658135.42it/s] 3443685it [00:02, 1659428.44it/s] 3610815it [00:02, 1662962.64it/s] 3777134it [00:02, 1659819.92it/s] 3943133it [00:02, 1650620.97it/s] 4108217it [00:02, 1633489.24it/s] 4274714it [00:02, 1642743.21it/s] 4439032it [00:02, 1641764.61it/s] 4603238it [00:02, 1641328.05it/s] 4767392it [00:02, 1629247.40it/s] 4930347it [00:03, 1610621.18it/s] 5094919it [00:03, 1620969.85it/s] 5262433it [00:03, 1637020.99it/s] 5429016it [00:03, 1645567.38it/s] 5601015it [00:03, 1667716.66it/s] 5770964it [00:03, 1677172.32it/s] 5940495it [00:03, 1682561.35it/s] 6108775it [00:03, 1675712.65it/s] 6276368it [00:03, 1670938.40it/s] 6443479it [00:03, 1669710.15it/s][W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai 6610462it [00:04, 1646743.77it/s] 6779730it [00:04, 1660327.89it/s] 6946948it [00:04, 1663831.65it/s] 7113381it [00:04, 1656409.57it/s] 7282568it [00:04, 1666947.15it/s] 7449572it [00:04, 1667800.58it/s] 7616750it [00:04, 1668969.03it/s] 7783665it [00:04, 1661092.47it/s] 7951612it [00:04, 1666554.03it/s] 8120935it [00:04, 1674505.60it/s] 8291045it [00:05, 1682442.44it/s] 8459302it [00:05, 1678578.94it/s] 8627170it [00:05, 1627875.43it/s] 8790286it [00:05, 1627551.23it/s] 8958042it [00:05, 1642246.11it/s] 9122968it [00:05, 1644303.45it/s] 9289660it [00:05, 1651008.27it/s] 9455580it [00:05, 1653348.25it/s] 9621561it [00:05, 1655137.64it/s] 9790200it [00:05, 1664466.68it/s] 9960108it [00:06, 1674811.30it/s] 10130050it [00:06, 1682060.89it/s] 10298278it [00:06, 1666493.55it/s] 10467822it [00:06, 1675090.91it/s] 10637540it [00:06, 1681662.65it/s] 10805737it [00:06, 1623264.73it/s] 10968961it [00:06, 1625766.04it/s] 11138517it [00:06, 1646280.27it/s] 11308897it [00:06, 1663199.18it/s] 11476015it [00:06, 1665548.65it/s] 11643714it [00:07, 1668937.18it/s] 11810798it [00:07, 1669485.61it/s] 11977821it [00:07, 1658923.10it/s] 12149026it [00:07, 1674606.26it/s] 12317909it [00:07, 1678825.63it/s] 12487297it [00:07, 1683298.18it/s] 12655841it [00:07, 1683918.04it/s] 12825580it [00:07, 1687882.15it/s] 12994384it [00:07, 1685312.51it/s] 13162927it [00:07, 1683653.48it/s] 13193971it [00:07, 1649326.15it/s] [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai tabix -s 1 -b 2 -e 2 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz > 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv cat 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md -output 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/659_cIX-T1-TRNA-1_B23WHTKLT4_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 2 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_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 2 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz> 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_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 2 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_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: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bai cat 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_cIX-T1-TRNA-1_B23WHTKLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md/qc_complete.txt + merge_qc -folders 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1.md -output 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv + head -n1 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_cIX-T1-TRNA-1_B23WHTKLT4_1/659_cIX-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv