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/72/0f66186e87b9dafe55cbf4319607ad/.command.sh 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/ea/8b7f8010f56998e5bc4bc55b31125b/aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/0f66186e87b9dafe55cbf4319607ad/.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/ea/8b7f8010f56998e5bc4bc55b31125b/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 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 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 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 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai 124505it [00:00, 1245003.69it/s] 259920it [00:00, 1308951.99it/s] 400786it [00:00, 1354374.44it/s] 539888it [00:00, 1368822.52it/s] 678593it [00:00, 1375378.87it/s] 817108it [00:00, 1378533.69it/s] 957234it [00:00, 1385951.10it/s] 1096229it [00:00, 1387210.78it/s] 1234951it [00:00, 1384141.01it/s] 1373552it [00:01, 1384531.30it/s] 1512954it [00:01, 1387418.13it/s] 1651697it [00:01, 1385986.84it/s] 1790297it [00:01, 1384181.07it/s] 1928717it [00:01, 1383646.11it/s] 2068066it [00:01, 1386597.24it/s] 2206727it [00:01, 1384940.50it/s] 2349564it [00:01, 1397966.26it/s] 2489364it [00:01, 1394910.25it/s] 2628859it [00:01, 1393743.65it/s] 2768236it [00:02, 1376399.59it/s] 2905923it [00:02, 1359527.44it/s] 3045520it [00:02, 1370267.18it/s] 3183675it [00:02, 1373592.19it/s] 3321948it [00:02, 1376290.44it/s] 3461572it [00:02, 1382221.80it/s] 3602924it [00:02, 1391557.23it/s] 3744397it [00:02, 1398471.97it/s] 3884485it [00:02, 1399170.45it/s] 4025429it [00:02, 1402213.58it/s] 4165660it [00:03, 1394445.71it/s] 4305121it [00:03, 1392822.20it/s] 4444414it [00:03, 1390817.77it/s] 4583504it [00:03, 1388566.23it/s] 4722366it [00:03, 1385156.06it/s] 4861416it [00:03, 1386738.73it/s] 5001486it [00:03, 1390834.18it/s] 5142216it [00:03, 1395750.43it/s] 5283615it [00:03, 1401197.17it/s] 5423739it [00:03, 1397534.94it/s] 5565013it [00:04, 1402005.95it/s] 5705218it [00:04, 1397731.69it/s] 5845172it [00:04, 1398257.76it/s] 5985126it [00:04, 1398628.93it/s] 6126006it [00:04, 1401662.44it/s] 6267275it [00:04, 1404890.86it/s] 6407767it [00:04, 1403355.57it/s] 6548105it [00:04, 1396875.97it/s] 6689545it [00:04, 1402098.48it/s] 6829763it [00:04, 1400351.66it/s] 6969988it [00:05, 1400907.89it/s] 7110083it [00:05, 1397726.40it/s] 7250099it [00:05, 1398440.69it/s] 7389946it [00:05, 1389476.95it/s] 7528907it [00:05, 1388079.14it/s] 7667724it [00:05, 1387581.26it/s] 7808056it [00:05, 1392271.83it/s] 7948867it [00:05, 1396945.49it/s] 8089930it [00:05, 1401030.59it/s] 8231288it [00:05, 1404716.63it/s] 8371764it [00:06, 1403381.24it/s] 8512105it [00:06, 1403327.10it/s] 8652440it [00:06, 1401274.70it/s] 8792570it [00:06, 1399926.22it/s] 8932564it [00:06, 1399440.20it/s] 9072639it [00:06, 1399819.93it/s] 9212622it [00:06, 1392901.81it/s] 9352409it [00:06, 1394372.45it/s] 9493264it [00:06, 1398600.50it/s] 9635432it [00:06, 1405490.22it/s] 9777555it [00:07, 1410192.51it/s] 9918579it [00:07, 1407113.52it/s] 10061242it [00:07, 1412943.52it/s] 10202541it [00:07, 1406518.51it/s] 10343202it [00:07, 1404626.58it/s] 10483671it [00:07, 1400140.31it/s] 10623691it [00:07, 1393221.01it/s] 10763022it [00:07, 1389986.05it/s] 10902027it [00:07, 1389819.84it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai 11041216it [00:07, 1390364.14it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.md.bai 11180257it [00:08, 1390365.37it/s] 11319296it [00:08, 1382930.36it/s] 11457598it [00:08, 1372459.50it/s] 11594863it [00:08, 1371804.82it/s] 11734094it [00:08, 1377902.57it/s] 11872706it [00:08, 1380342.77it/s] 12011785it [00:08, 1383453.10it/s] 12150973it [00:08, 1385961.81it/s] 12291821it [00:08, 1392695.62it/s] 12433454it [00:08, 1399763.14it/s] 12573435it [00:09, 1394975.28it/s] 12715202it [00:09, 1401751.85it/s] 12856849it [00:09, 1406129.36it/s] 12997572it [00:09, 1406321.86it/s] 13138749it [00:09, 1407942.83it/s] 13279547it [00:09, 1405452.23it/s] 13420096it [00:09, 1403697.05it/s] 13525934it [00:09, 1392346.08it/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 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