Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/00484fe852162b8e110fc737289ac9/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai 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/90/bc39f89f7d94a3839807c4d4c9a31c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/00484fe852162b8e110fc737289ac9/659_bTq-T1-TRNA-1_B23MHV2LT4_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-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/bc39f89f7d94a3839807c4d4c9a31c/.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_bTq-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bTq-T1-TRNA-1_B23MHV2LT4_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_bTq-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_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_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_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_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai 130532it [00:00, 1305193.66it/s] 270967it [00:00, 1363496.41it/s] 411828it [00:00, 1384069.08it/s] 550236it [00:00, 1375701.47it/s] 687814it [00:00, 1369705.50it/s] 824792it [00:00, 1365766.16it/s] 965144it [00:00, 1378021.55it/s] 1104999it [00:00, 1384511.13it/s] 1246472it [00:00, 1393912.54it/s] 1386166it [00:01, 1394829.46it/s] 1527781it [00:01, 1401329.25it/s] 1668576it [00:01, 1403325.66it/s] 1808913it [00:01, 1403143.01it/s] 1949230it [00:01, 1396844.84it/s] 2093088it [00:01, 1409365.03it/s] 2235099it [00:01, 1412575.50it/s] 2378593it [00:01, 1419272.95it/s] 2520748it [00:01, 1419934.39it/s] 2662747it [00:01, 1413327.34it/s] 2807351it [00:02, 1423095.08it/s] 2951266it [00:02, 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1446752.45it/s] 7258424it [00:05, 1447088.13it/s] 7403138it [00:05, 1445761.88it/s] 7547718it [00:05, 1439488.38it/s] 7691675it [00:05, 1437574.31it/s] 7835438it [00:05, 1435457.48it/s] 7979434it [00:05, 1436784.32it/s] 8125271it [00:05, 1443222.38it/s] 8269597it [00:05, 1442001.68it/s] 8414628it [00:05, 1444469.35it/s] 8559078it [00:06, 1442081.88it/s] 8703747it [00:06, 1443445.37it/s] 8848272it [00:06, 1443924.51it/s] 8992666it [00:06, 1441331.29it/s] 9138414it [00:06, 1446149.09it/s] 9283032it [00:06, 1443965.08it/s] 9427431it [00:06, 1439430.58it/s] 9571795it [00:06, 1440674.85it/s] 9715866it [00:06, 1435570.02it/s] 9860539it [00:06, 1438887.71it/s] 10008551it [00:07, 1451166.84it/s] 10153675it [00:07, 1448630.17it/s] 10298544it [00:07, 1443434.53it/s] 10444770it [00:07, 1449037.97it/s] 10589682it [00:07, 1443731.54it/s] 10734159it [00:07, 1444023.50it/s] 10883684it [00:07, 1459212.54it/s] 11029615it [00:07, 1453181.46it/s] 11174944it [00:07, 1438857.97it/s] 11320150it [00:07, 1442707.32it/s] 11464448it [00:08, 1441487.88it/s] 11608616it [00:08, 1439444.86it/s] 11752573it [00:08, 1436118.96it/s] 11896602it [00:08, 1437251.77it/s] 12042113it [00:08, 1442440.03it/s] 12186364it [00:08, 1442186.68it/s] 12330588it [00:08, 1437812.23it/s] 12474375it [00:08, 1433484.60it/s] 12618261it [00:08, 1434911.46it/s] 12761757it [00:08, 1434077.83it/s] 12905190it [00:09, 1434135.27it/s] 13048606it [00:09, 1431542.20it/s] 13191835it [00:09, 1431750.02it/s] 13335012it [00:09, 1431380.35it/s] 13481864it [00:09, 1442486.70it/s][W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai 13628307it [00:09, 1449044.63it/s] 13775547it [00:09, 1456023.61it/s] 13921152it [00:09, 1442023.40it/s] 14065644it [00:09, 1442863.04it/s] 14209953it [00:09, 1441549.29it/s] 14358297it [00:10, 1454041.61it/s] 14505691it [00:10, 1459877.39it/s] 14509018it [00:10, 1428666.96it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/659_bTq-T1-TRNA-1_B23MHV2LT4_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_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_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_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_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_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_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_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_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_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bTq-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bTq-T1-TRNA-1_B23MHV2LT4_1/659_bTq-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv