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/32/8d334734c1317d2dfe2a88e2c4e992/.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/90/a11eaca8b79ddf77e7c19eae46a21d/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/8d334734c1317d2dfe2a88e2c4e992/.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/90/a11eaca8b79ddf77e7c19eae46a21d/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-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-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bai 115761it [00:00, 1157500.72it/s] 241872it [00:00, 1218396.12it/s] 367640it [00:00, 1236290.66it/s] 495946it [00:00, 1254720.03it/s] 623158it [00:00, 1260861.40it/s] 750671it [00:00, 1265566.99it/s] 879629it [00:00, 1273384.91it/s] 1006968it [00:00, 1271197.92it/s] 1134482it [00:00, 1272401.63it/s] 1263636it [00:01, 1278277.91it/s] 1392181it [00:01, 1280443.92it/s] 1521399it [00:01, 1283982.19it/s] 1649798it [00:01, 1275689.82it/s] 1777529it [00:01, 1276143.39it/s] 1905153it [00:01, 1276132.56it/s] 2032773it [00:01, 1273140.66it/s] 2160093it [00:01, 1266182.21it/s] 2288990it [00:01, 1272968.94it/s] 2416299it [00:01, 1032643.52it/s] 2545609it [00:02, 1099658.30it/s] 2673549it [00:02, 1147962.53it/s] 2799491it [00:02, 1178872.37it/s] 2925024it [00:02, 1200558.18it/s] 3052001it [00:02, 1220503.64it/s] 3176404it [00:02, 1227273.09it/s] 3300535it [00:02, 1217451.54it/s] 3423270it [00:02, 1208138.54it/s] 3544779it [00:02, 1205052.57it/s] 3665767it [00:02, 1200502.32it/s] 3786534it [00:03, 1202593.89it/s] 3907906it [00:03, 1205781.72it/s] 4028655it [00:03, 1206034.53it/s] 4154187it [00:03, 1220704.57it/s] 4280822it [00:03, 1234316.13it/s] 4408160it [00:03, 1245984.45it/s] 4536602it [00:03, 1257467.48it/s] 4663433it [00:03, 1260691.55it/s] 4791686it [00:03, 1267187.78it/s] 4918425it [00:03, 1259182.41it/s] 5046481it [00:04, 1265541.54it/s] 5173056it [00:04, 1264966.79it/s] 5300165it [00:04, 1266774.55it/s] 5427020it [00:04, 1267282.07it/s] 5554695it [00:04, 1270059.86it/s] 5682132it [00:04, 1271323.80it/s] 5811034it [00:04, 1276604.54it/s] 5938698it [00:04, 1274805.62it/s] 6066844it [00:04, 1276774.97it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai 6195104it [00:04, 1278492.84it/s] 6322955it [00:05, 1270093.79it/s] 6449978it [00:05, 1266456.00it/s] 6576634it [00:05, 1266141.58it/s] 6703868it [00:05, 1267964.91it/s] 6831972it [00:05, 1271851.03it/s] 6959540it [00:05, 1272972.30it/s] 7086841it [00:05, 1264199.46it/s] 7213284it [00:05, 1264247.90it/s] 7339908it [00:05, 1264821.81it/s] 7466398it [00:06, 1263886.49it/s] 7592792it [00:06, 1263009.00it/s] 7719097it [00:06, 1258950.03it/s] 7844997it [00:06, 1254423.17it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai 7972718it [00:06, 1261197.82it/s] 8100443it [00:06, 1265969.95it/s] 8228060it [00:06, 1268585.27it/s] 8356264it [00:06, 1272593.77it/s] 8484564it [00:06, 1275680.49it/s] 8613540it [00:06, 1279878.40it/s] 8742618it [00:07, 1283120.24it/s] 8871368it [00:07, 1284409.05it/s] 8999811it [00:07, 1280145.92it/s] 9127830it [00:07, 1279569.78it/s] 9255790it [00:07, 1268698.69it/s] 9382681it [00:07, 1262860.13it/s] 9510441it [00:07, 1267209.88it/s] 9638557it [00:07, 1271346.77it/s] 9766039it [00:07, 1272359.35it/s] 9893285it [00:07, 1270641.86it/s] 10020427it [00:08, 1270848.68it/s] 10147517it [00:08, 1265619.82it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai 10275482it [00:08, 1269785.44it/s] 10404507it [00:08, 1275762.48it/s] 10532090it [00:08, 1269485.65it/s] 10659049it [00:08, 1266822.44it/s] 10785921it [00:08, 1267244.02it/s] 10915010it [00:08, 1274282.73it/s] 11042445it [00:08, 1273655.33it/s] 11171478it [00:08, 1278624.63it/s] 11299345it [00:09, 1277762.53it/s] 11427125it [00:09, 1274344.01it/s] 11555222it [00:09, 1276299.91it/s] 11556068it [00:09, 1253661.07it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md -output aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md -output aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1_full_basic_stats.tsv