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/86/0f2394b8b01427261d5321d628f994/.command.sh 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/6a/2eed140207f1dfe0aa42363cf40b15/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bam 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/86/0f2394b8b01427261d5321d628f994/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/2eed140207f1dfe0aa42363cf40b15/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai 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 aih-tih-sc-1351d2-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai 0it [00:00, ?it/s] 80953it [00:00, 809413.05it/s] 174989it [00:00, 886389.35it/s] 295761it [00:00, 1032925.02it/s] 419294it [00:00, 1112784.54it/s] 537901it [00:00, 1139176.91it/s] 661418it [00:00, 1171784.44it/s] 782603it [00:00, 1184853.54it/s] 903479it [00:00, 1192389.84it/s] 1027892it [00:00, 1208533.78it/s] 1151094it [00:01, 1215748.45it/s] 1273672it [00:01, 1218789.40it/s] 1397941it [00:01, 1225956.05it/s] 1520537it [00:01, 1225908.91it/s] 1643496it [00:01, 1226997.16it/s] 1766196it [00:01, 1216776.82it/s] 1888515it [00:01, 1218564.88it/s] 2012883it [00:01, 1225998.05it/s] 2135496it [00:01, 1222188.09it/s] 2257726it [00:01, 1215350.23it/s] 2379275it [00:02, 1201953.11it/s] 2500445it [00:02, 1204815.87it/s] 2620955it [00:02, 1203622.05it/s] 2741336it [00:02, 1200546.37it/s] 2861404it [00:02, 1162332.70it/s] 2979572it [00:02, 1167860.05it/s] 3099529it [00:02, 1177034.34it/s] 3220024it [00:02, 1185268.12it/s] 3341040it [00:02, 1192637.63it/s] 3461247it [00:02, 1195423.18it/s] 3582536it [00:03, 1200609.72it/s] 3704057it [00:03, 1204905.12it/s] 3827150it [00:03, 1212668.42it/s] 3949373it [00:03, 1215429.15it/s] 4071707it [00:03, 1217768.50it/s] 4193498it [00:03, 1213513.39it/s] 4314862it [00:03, 1212662.70it/s] 4436137it [00:03, 1203457.97it/s] 4557522it [00:03, 1206530.31it/s] 4678377it [00:03, 1207112.02it/s] 4799100it [00:04, 1183820.62it/s] 4917769it [00:04, 1184640.41it/s] 5037700it [00:04, 1188963.17it/s] 5156652it [00:04, 1185462.67it/s] 5278618it [00:04, 1195616.40it/s] 5401614it [00:04, 1205836.20it/s] 5524451it [00:04, 1212519.77it/s] 5645727it [00:04, 1202787.20it/s] 5766038it [00:04, 1199434.60it/s] 5886004it [00:04, 1198854.29it/s] 6005905it [00:05, 1195204.56it/s] 6126664it [00:05, 1198870.05it/s] 6249188it [00:05, 1206721.22it/s] 6369871it [00:05, 1204837.24it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai 6491695it [00:05, 1208821.40it/s] 6613150it [00:05, 1210509.67it/s] 6734828it [00:05, 1212361.27it/s] 6856068it [00:05, 1203937.76it/s] 6977394it [00:05, 1206578.18it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai 7099034it [00:05, 1209391.64it/s] 7222737it [00:06, 1217626.33it/s] 7345822it [00:06, 1221559.45it/s] 7468167it [00:06, 1222099.08it/s] 7590382it [00:06, 1219644.99it/s] 7712351it [00:06, 1218992.37it/s] 7835900it [00:06, 1223904.74it/s] 7959384it [00:06, 1227050.70it/s] 8082092it [00:06, 1218856.67it/s] 8203992it [00:06, 1216385.99it/s] 8327063it [00:06, 1220633.31it/s] 8450600it [00:07, 1224982.54it/s] 8577595it [00:07, 1238410.55it/s] 8701445it [00:07, 1233191.26it/s] 8824824it [00:07, 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[00:10, 1224219.26it/s] 12488289it [00:10, 1228666.06it/s] 12579689it [00:10, 1201048.81it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md -output aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1.md -output aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_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-1351d2-R1_A23WJ53LT4_1/aih-tih-sc-1351d2-R1_A23WJ53LT4_1_full_basic_stats.tsv