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/81/5327333eaa0fcad2df02a3d48bb44d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/2595d340b0d3b0e1df94ed6ea35beb/aih-tih-sc-51d534-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/20/2595d340b0d3b0e1df94ed6ea35beb/aih-tih-sc-51d534-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/81/5327333eaa0fcad2df02a3d48bb44d/.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-51d534-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-51d534-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-51d534-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-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-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-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-51d534-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-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-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-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-51d534-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-51d534-R1_B23WHYVLT4_1.md.bai 94524it [00:00, 945168.79it/s] 196249it [00:00, 987538.27it/s] 296571it [00:00, 994676.33it/s] 399603it [00:00, 1008720.43it/s] 502133it [00:00, 1014678.32it/s] 604937it [00:00, 1019204.11it/s] 708159it [00:00, 1023437.13it/s] 810701it [00:00, 1024049.24it/s] 913368it [00:00, 1024755.76it/s] 1015943it [00:01, 1025046.38it/s] 1118506it [00:01, 1025203.59it/s] 1221027it [00:01, 1018487.08it/s] 1324330it [00:01, 1022856.37it/s] 1426625it [00:01, 1018095.97it/s] 1528757it [00:01, 1019000.07it/s] 1630665it [00:01, 1015770.67it/s] 1732249it [00:01, 1006015.91it/s] 1832872it [00:01, 1003484.78it/s] 1935478it [00:01, 1010189.46it/s] 2036513it [00:02, 1006526.85it/s] 2138970it [00:02, 1011797.40it/s] 2240162it [00:02, 995521.57it/s] 2339774it [00:02, 992027.06it/s] 2439017it [00:02, 951683.93it/s] 2534522it [00:02, 932058.49it/s] 2627989it [00:02, 845833.73it/s] 2714069it [00:02, 847678.40it/s] 2799902it [00:02, 848164.87it/s] 2888560it [00:02, 859063.03it/s] 2975051it [00:03, 857659.76it/s] 3066037it [00:03, 872843.87it/s] 3153650it [00:03, 808562.38it/s] 3248879it [00:03, 848758.15it/s] 3352134it [00:03, 901113.53it/s] 3459118it [00:03, 949945.53it/s] 3563490it [00:03, 977372.77it/s] 3665811it [00:03, 990866.81it/s] 3768605it [00:03, 1001832.74it/s] 3869152it [00:04, 995046.10it/s] 3971311it [00:04, 1002897.79it/s] 4074143it [00:04, 1010443.92it/s] 4175328it [00:04, 1003064.24it/s] 4275742it [00:04, 1001719.82it/s] 4375989it [00:04, 991756.30it/s] 4477417it [00:04, 998410.59it/s] 4578856it [00:04, 1003144.60it/s] 4679214it [00:04, 1001951.42it/s] 4779440it [00:04, 989887.77it/s] 4878477it [00:05, 980472.65it/s] 4976568it [00:05, 979319.22it/s] 5074529it [00:05, 968186.83it/s] 5171385it [00:05, 955805.76it/s] 5268834it [00:05, 961203.96it/s] 5370292it [00:05, 976913.48it/s] 5470162it [00:05, 983366.31it/s] 5570354it [00:05, 988859.04it/s] 5669891it [00:05, 990784.40it/s] 5768995it [00:05, 989610.58it/s] 5867974it [00:06, 981491.23it/s] 5966148it [00:06, 974913.46it/s] 6063891it [00:06, 975527.54it/s] 6161461it [00:06, 973041.19it/s] 6258777it [00:06, 972521.53it/s] 6356037it [00:06, 972025.18it/s] 6453430it [00:06, 972580.01it/s] 6551263it [00:06, 974234.98it/s] 6650685it [00:06, 980113.40it/s] 6750935it [00:06, 986802.49it/s] 6849823it [00:07, 987411.24it/s] 6948567it [00:07, 972283.18it/s] 7046776it [00:07, 975148.08it/s] 7144749it [00:07, 976497.42it/s] 7243336it [00:07, 979278.38it/s] 7343387it [00:07, 985535.97it/s] 7441959it [00:07, 983662.65it/s] 7544385it [00:07, 995746.00it/s] 7643973it [00:07, 994651.52it/s] 7743448it [00:07, 947914.51it/s] 7838699it [00:08, 921153.82it/s] 7931227it [00:08, 918100.67it/s] 8023315it [00:08, 894590.42it/s] 8113031it [00:08, 893214.77it/s] 8202527it [00:08, 884306.04it/s] 8291073it [00:08, 864114.84it/s] 8377614it [00:08, 853284.40it/s] 8463148it [00:08, 853864.69it/s] 8549870it [00:08, 857757.04it/s] 8635698it [00:09, 856765.31it/s] 8722039it [00:09, 858712.83it/s] 8807938it [00:09, 847879.09it/s] 8892767it [00:09, 836880.79it/s] 8983966it [00:09, 858946.96it/s] 9083669it [00:09, 899766.93it/s] 9181835it [00:09, 924073.36it/s] 9280312it [00:09, 942136.29it/s] 9377362it [00:09, 950586.82it/s] 9475034it [00:09, 958384.84it/s] 9573812it [00:10, 967091.05it/s] 9673222it [00:10, 975161.53it/s] 9774537it [00:10, 986529.94it/s] 9875850it [00:10, 994485.38it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai 9978516it [00:10, 1004116.13it/s] 10081733it [00:10, 1012508.48it/s] 10182992it [00:10, 1011097.43it/s] 10284108it [00:10, 1004366.24it/s] 10384559it [00:10, 1002974.75it/s] 10484866it [00:10, 998702.88it/s] 10584745it [00:11, 993552.15it/s] 10684110it [00:11, 985731.68it/s] 10782698it [00:11, 979541.15it/s] 10880665it [00:11, 975322.82it/s] 10978205it [00:11, 971671.17it/s] 11075377it [00:11, 966327.88it/s] 11172853it [00:11, 968813.74it/s] 11271846it [00:11, 975054.28it/s] 11369361it [00:11, 956738.22it/s] 11465109it [00:11, 914630.92it/s] 11556961it [00:12, 899961.72it/s] 11647226it [00:12, 887607.41it/s] 11739923it [00:12, 898830.57it/s] 11839910it [00:12, 928261.86it/s] 11939713it [00:12, 948724.33it/s] 12039254it [00:12, 962461.95it/s] 12138875it [00:12, 972469.45it/s] 12238729it [00:12, 980221.54it/s] 12338712it [00:12, 986062.42it/s] 12438389it [00:12, 989248.92it/s] 12538648it [00:13, 993226.79it/s] 12639762it [00:13, 998573.88it/s] 12739644it [00:13, 996019.51it/s] 12839264it [00:13, 995136.08it/s] 12938791it [00:13, 980154.66it/s] 13036863it [00:13, 945855.46it/s] 13131713it [00:13, 928945.79it/s] 13225348it [00:13, 930921.12it/s] 13318590it [00:13, 891580.15it/s] 13417249it [00:13, 918607.12it/s] 13516259it [00:14, 939300.58it/s] 13616141it [00:14, 956706.65it/s] 13716252it [00:14, 969783.44it/s] 13816130it [00:14, 978359.48it/s] 13915439it [00:14, 982725.97it/s] 14016381it [00:14, 990669.64it/s] 14118260it [00:14, 999052.74it/s] 14218642it [00:14, 1000463.99it/s] 14320866it [00:14, 1006966.21it/s] 14422853it [00:14, 1010809.56it/s] 14525075it [00:15, 1014212.73it/s] 14626803it [00:15, 1015116.55it/s] 14728602it [00:15, 1015960.26it/s] 14830674it [00:15, 1017371.20it/s] 14932552it [00:15, 1017778.00it/s] 15034657it [00:15, 1018742.93it/s] 15136535it [00:15, 1006088.30it/s] 15237537it [00:15, 1007137.00it/s] 15338278it [00:15, 1002836.54it/s] 15438583it [00:16, 1000883.13it/s] 15538686it [00:16, 995785.66it/s] 15638503it [00:16, 996480.50it/s] 15738583it [00:16, 997753.52it/s] 15838366it [00:16, 991886.75it/s] 15939178it [00:16, 996704.57it/s] 16038860it [00:16, 995304.80it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai 16138398it [00:16, 982449.07it/s] 16236681it [00:16, 978707.19it/s] 16334577it [00:16, 977420.78it/s] 16432336it [00:17, 971290.42it/s] 16531263it [00:17, 976611.11it/s] 16632654it [00:17, 987697.44it/s] 16732812it [00:17, 991822.86it/s] 16832011it [00:17, 982581.61it/s] 16931272it [00:17, 985546.76it/s] 17029849it [00:17, 982459.21it/s] 17128111it [00:17, 972548.47it/s] 17225394it [00:17, 960144.25it/s] 17321451it [00:17, 936734.25it/s] 17415245it [00:18, 936337.38it/s] 17508962it [00:18, 897798.03it/s] 17599073it [00:18, 892023.26it/s] 17700256it [00:18, 926642.57it/s] 17801080it [00:18, 950431.28it/s] 17901995it [00:18, 967709.67it/s] 18003541it [00:18, 981837.87it/s] 18105881it [00:18, 994177.93it/s] 18208361it [00:18, 1003292.21it/s] 18309297it [00:18, 1004984.48it/s] 18409864it [00:19, 1004992.01it/s] 18510954it [00:19, 1006746.09it/s] 18611663it [00:19, 1003175.37it/s] 18712007it [00:19, 998859.56it/s] 18811914it [00:19, 997146.16it/s] 18912194it [00:19, 998815.97it/s] 19012260it [00:19, 999350.34it/s] 19114371it [00:19, 1005842.97it/s] 19214964it [00:19, 1005844.90it/s] 19315554it [00:19, 1005455.18it/s] 19416104it [00:20, 989476.29it/s] 19515650it [00:20, 991233.31it/s] 19616285it [00:20, 995713.32it/s] 19717763it [00:20, 1001379.67it/s] 19818661it [00:20, 1003630.51it/s] 19919154it [00:20, 1004003.03it/s] 20019569it [00:20, 1003325.44it/s] 20120122it [00:20, 1003969.32it/s] 20220526it [00:20, 1001753.35it/s] 20320708it [00:20, 999824.78it/s] 20421247it [00:21, 1001472.98it/s] 20521398it [00:21, 997075.33it/s] 20622758it [00:21, 1001994.38it/s] 20723840it [00:21, 1004618.69it/s] 20824308it [00:21, 1003438.63it/s] 20926076it [00:21, 1007685.81it/s] 21028610it [00:21, 1012960.95it/s] 21130955it [00:21, 1016089.63it/s] 21233562it [00:21, 1019063.98it/s] 21335471it [00:21, 1017971.12it/s] 21437270it [00:22, 1015639.97it/s] 21538837it [00:22, 1009853.20it/s] 21639831it [00:22, 1005073.17it/s] 21740347it [00:22, 974319.91it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai 21837971it [00:22, 967192.28it/s] 21940364it [00:22, 983759.37it/s] 22043229it [00:22, 996934.52it/s] 22144536it [00:22, 1001657.28it/s] 22244788it [00:22, 1000894.94it/s] 22344938it [00:22, 997724.16it/s] 22445748it [00:23, 1000799.61it/s] 22547784it [00:23, 1006620.29it/s] 22648517it [00:23, 1006815.53it/s] 22749221it [00:23, 1006867.90it/s] 22851671it [00:23, 1012062.67it/s] 22952887it [00:23, 854348.30it/s] 23007140it [00:23, 969016.26it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-51d534-R1_B23WHYVLT4_1.md -output aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/aih-tih-sc-51d534-R1_B23WHYVLT4_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-51d534-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_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-51d534-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_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-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_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-51d534-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_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-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-51d534-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_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-51d534-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1.md -output aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_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-51d534-R1_B23WHYVLT4_1/aih-tih-sc-51d534-R1_B23WHYVLT4_1_full_basic_stats.tsv