Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/2230ee04bfb2133305f2233da27c01/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz 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/3c/a8f0635560f20b28556929779154c0/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/2230ee04bfb2133305f2233da27c01/.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-rnd-pltf-dev-nextflow-scratch-01/work/3c/a8f0635560f20b28556929779154c0/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir aih-tih-sc-3abdf4-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 126855it [00:00, 1268415.12it/s] 262392it [00:00, 1319506.19it/s] 401043it [00:00, 1350058.06it/s] 538411it [00:00, 1359347.98it/s] 677640it [00:00, 1371197.56it/s] 814760it [00:00, 1371057.69it/s] 951866it [00:00, 1361945.19it/s] 1088073it [00:00, 1348498.16it/s] 1222954it [00:00, 1346195.15it/s] 1357593it [00:01, 1336820.77it/s] 1496005it [00:01, 1351009.17it/s] 1635836it [00:01, 1365267.66it/s] 1775139it [00:01, 1373611.85it/s] 1916583it [00:01, 1385874.54it/s] 2057356it [00:01, 1392290.30it/s] 2196768it [00:01, 1392812.47it/s] 2340393it [00:01, 1405834.11it/s] 2480987it [00:01, 1405152.23it/s] 2621510it [00:01, 1401097.71it/s] 2761628it [00:02, 1389533.89it/s] 2902220it [00:02, 1394390.17it/s] 3042903it [00:02, 1398072.88it/s] 3182727it [00:02, 1397743.69it/s] 3322513it [00:02, 1395572.81it/s] 3462079it [00:02, 1234102.66it/s] 3603690it [00:02, 1283993.30it/s] 3745607it [00:02, 1322022.99it/s] 3886714it [00:02, 1347542.66it/s] 4029006it [00:02, 1369383.24it/s] 4169255it [00:03, 1379071.91it/s] 4310607it [00:03, 1389224.05it/s] 4450176it [00:03, 1384505.51it/s] 4590776it [00:03, 1390861.42it/s] 4733803it [00:03, 1402571.70it/s] 4875027it [00:03, 1405434.76it/s] 5015738it [00:03, 1403237.29it/s] 5156958it [00:03, 1405876.60it/s] 5298039it [00:03, 1407316.68it/s] 5438830it [00:03, 1399581.28it/s] 5581247it [00:04, 1406897.83it/s] 5721976it [00:04, 1401379.47it/s] 5862144it [00:04, 1398704.46it/s] 6002036it [00:04, 1215882.78it/s] 6140318it [00:04, 1261005.67it/s] 6280188it [00:04, 1299356.04it/s] 6418388it [00:04, 1322869.70it/s] 6555780it [00:04, 1337613.91it/s] 6694195it [00:04, 1351163.51it/s] 6834684it [00:05, 1366967.82it/s] 6975314it [00:05, 1378596.86it/s] 7114703it [00:05, 1383122.45it/s] 7254574it [00:05, 1387750.86it/s] 7395917it [00:05, 1395319.48it/s] 7537755it [00:05, 1402193.19it/s] 7678116it [00:05, 1401198.71it/s] 7818335it [00:05, 1394741.47it/s] 7957885it [00:05, 1388079.63it/s] 8096750it [00:05, 1382250.12it/s] 8235017it [00:06, 1374082.50it/s] 8372460it [00:06, 1370205.07it/s] 8509504it [00:06, 1352395.60it/s] 8644798it [00:06, 1323128.02it/s] 8779068it [00:06, 1328806.43it/s] 8917988it [00:06, 1346511.45it/s] 9057045it [00:06, 1359458.97it/s] 9195080it [00:06, 1365646.92it/s] 9334519it [00:06, 1374190.21it/s] 9474423it [00:06, 1381590.08it/s] 9612625it [00:07, 1364433.26it/s] 9749142it [00:07, 1363417.73it/s] 9885623it [00:07, 1363734.61it/s] 10025788it [00:07, 1375018.81it/s] 10164980it [00:07, 1380046.83it/s] 10303009it [00:07, 1375185.91it/s] 10440548it [00:07, 1366713.18it/s] 10577242it [00:07, 1350119.26it/s] 10712304it [00:07, 1338077.20it/s] 10846659it [00:07, 1339661.06it/s] 10980659it [00:08, 1318953.39it/s] 11119783it [00:08, 1340210.46it/s] 11256487it [00:08, 1348012.29it/s] 11391364it [00:08, 1305506.91it/s] 11522227it [00:08, 1250368.29it/s] 11660846it [00:08, 1289040.69it/s] 11796398it [00:08, 1308247.72it/s] 11927728it [00:08, 1292456.58it/s] 12060519it [00:08, 1302782.25it/s] 12198550it [00:08, 1325484.53it/s] 12339113it [00:09, 1349181.50it/s] 12478702it [00:09, 1363038.88it/s] 12616724it [00:09, 1367992.92it/s] 12757134it [00:09, 1378654.93it/s] 12898295it [00:09, 1388487.36it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai 13037823it [00:09, 1390384.74it/s] 13176905it [00:09, 1386503.14it/s] 13315588it [00:09, 1370325.24it/s] 13453947it [00:09, 1374212.66it/s] 13525934it [00:09, 1360566.25it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md -output aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md -output aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-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-3abdf4-R1_A23YTGFLT4_1/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1_full_basic_stats.tsv