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/df/5de852b7b1ec69f33104f4a4e7bfbe/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/394b85d794d2913eac75122435dc8e/aih-tih-sc-c9a01b-R1_B23WHYVLT4_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-rnd-pltf-dev-nextflow-scratch-01/work/6c/394b85d794d2913eac75122435dc8e/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai 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/df/5de852b7b1ec69f33104f4a4e7bfbe/.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 aih-tih-sc-c9a01b-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-c9a01b-R1_B23WHYVLT4_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-c9a01b-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_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-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/full_bed.bed saturation_plot -bams aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_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-c9a01b-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_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-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_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-c9a01b-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai 115755it [00:00, 1157476.59it/s] 239141it [00:00, 1202370.41it/s] 363201it [00:00, 1219783.02it/s] 488398it [00:00, 1232434.36it/s] 614163it [00:00, 1241500.55it/s] 738519it [00:00, 1242076.29it/s] 863826it [00:00, 1245640.32it/s] 988391it [00:00, 1245007.87it/s] 1112892it [00:00, 1244642.62it/s] 1237357it [00:01, 1242676.03it/s] 1362630it [00:01, 1245720.87it/s] 1488434it [00:01, 1249436.98it/s] 1613379it [00:01, 1249011.29it/s] 1738281it [00:01, 1248574.92it/s] 1864045it [00:01, 1251275.13it/s] 1989174it [00:01, 1249856.40it/s] 2114161it [00:01, 1246862.65it/s] 2238850it [00:01, 1242250.48it/s] 2363080it [00:01, 1237075.17it/s] 2486794it [00:02, 1215587.70it/s] 2611055it [00:02, 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1253198.27it/s] 6356188it [00:05, 1249130.89it/s] 6481106it [00:05, 1248908.99it/s] 6606001it [00:05, 1243525.22it/s] 6730360it [00:05, 1243360.77it/s] 6856345it [00:05, 1248263.31it/s] 6981864it [00:05, 1250312.80it/s] 7106900it [00:05, 1244858.49it/s] 7232451it [00:05, 1247899.56it/s] 7357885it [00:05, 1249688.08it/s] 7482859it [00:06, 1247196.55it/s] 7607583it [00:06, 1245930.41it/s] 7732179it [00:06, 1244050.46it/s] 7859228it [00:06, 1251930.26it/s] 7985452it [00:06, 1254993.69it/s] 8111864it [00:06, 1257697.30it/s] 8237637it [00:06, 1256295.51it/s] 8367117it [00:06, 1267755.27it/s] 8493896it [00:06, 1245458.91it/s] 8618535it [00:06, 1245713.81it/s] 8743297it [00:07, 1246259.53it/s] 8868366it [00:07, 1247555.55it/s] 8993247it [00:07, 1247904.75it/s] 9118060it [00:07, 1244558.99it/s] 9242533it [00:07, 1242452.89it/s] 9366790it [00:07, 1238179.90it/s] 9491076it [00:07, 1239552.99it/s] 9615231it [00:07, 1240066.26it/s] 9739244it [00:07, 1239148.71it/s] 9864744it [00:07, 1243865.52it/s] 9990896it [00:08, 1249057.80it/s] 10115882it [00:08, 1249209.28it/s] 10240806it [00:08, 1247662.15it/s] 10365575it [00:08, 1242218.38it/s] 10489803it [00:08, 1241836.43it/s] 10613991it [00:08, 1241586.00it/s] 10738364it [00:08, 1242199.69it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai 10862587it [00:08, 1236823.45it/s] 10986276it [00:08, 1234460.02it/s] 11109727it [00:08, 1232288.26it/s] 11232959it [00:09, 1229159.66it/s] 11358479it [00:09, 1236911.20it/s] 11484780it [00:09, 1244690.16it/s] 11609721it [00:09, 1246075.56it/s] 11734334it [00:09, 1245158.64it/s] 11858854it [00:09, 1243443.58it/s] 11983201it [00:09, 1237113.18it/s] 12106921it [00:09, 1226482.65it/s] 12230841it [00:09, 1230236.33it/s] 12353884it [00:09, 1227923.34it/s] 12477194it [00:10, 1229447.14it/s] 12603055it [00:10, 1238136.90it/s] 12727605it [00:10, 1240316.54it/s] 12852529it [00:10, 1242966.08it/s] 12978397it [00:10, 1247650.38it/s] 13103168it [00:10, 1244291.14it/s] 13218360it [00:10, 1241905.71it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md -output aih-tih-sc-c9a01b-R1_B23WHYVLT4_1/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.md.depth.png