Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/d8208a6e5551fc5cd40705b4869524/aih-tih-sc-6e7384-R1_B23WHYVLT4_1_2.fastp.fastq.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/23ea377b86d622c23469aff6a9c2ee/aih-tih-sc-6e7384-R1_B23WHYVLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/110af4d6b683e83542fad5550ed441/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/110af4d6b683e83542fad5550ed441/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/d8208a6e5551fc5cd40705b4869524/aih-tih-sc-6e7384-R1_B23WHYVLT4_1_1.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.S9Grg66SOP/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.S9Grg66SOP/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.S9Grg66SOP/./star-fusion.preliminary -sample contains 295501023 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.S9Grg66SOP/ctat_genome_lib_build_dir -J /tmp/nxf.S9Grg66SOP/aih-tih-sc-6e7384-R1_B23WHYVLT4_1.Chimeric.out.junction -O /tmp/nxf.S9Grg66SOP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.S9Grg66SOP/aih-tih-sc-6e7384-R1_B23WHYVLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.S9Grg66SOP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=37500.00/min [20000], rate=38709.68/min [30000], rate=38297.87/min [40000], rate=39344.26/min [50000], rate=40540.54/min [60000], rate=41379.31/min [70000], rate=42857.14/min [80000], rate=43243.24/min [90000], rate=44262.30/min [100000], rate=45112.78/min [110000], rate=45517.24/min [120000], rate=46451.61/min [130000], rate=47272.73/min [140000], rate=48275.86/min [150000], rate=49180.33/min [160000], rate=50000.00/min [170000], rate=50746.27/min [180000], rate=51674.64/min [190000], rate=52293.58/min [200000], rate=53097.35/min [210000], rate=53389.83/min [220000], rate=54320.99/min [230000], rate=55200.00/min [240000], rate=56031.13/min [250000], rate=56603.77/min [260000], rate=57142.86/min [270000], rate=58064.52/min [280000], rate=56949.15/min [290000], rate=55414.01/min [300000], rate=53892.22/min [310000], rate=52991.45/min [320000], rate=52032.52/min [330000], rate=51162.79/min [340000], rate=49275.36/min [350000], rate=46770.60/min [360000], rate=45093.95/min [370000], rate=43700.79/min [380000], rate=42458.10/min [390000], rate=41269.84/min [400000], rate=40472.18/min [410000], rate=39935.06/min [420000], rate=39747.63/min [430000], rate=39753.47/min [440000], rate=39285.71/min [450000], rate=38737.45/min [460000], rate=38227.15/min [470000], rate=38159.68/min [480000], rate=37696.34/min [490000], rate=37404.58/min [500000], rate=37082.82/min [510000], rate=36646.71/min [520000], rate=36363.64/min [530000], rate=36095.35/min [540000], rate=35880.40/min [550000], rate=35714.29/min [560000], rate=35517.97/min [570000], rate=35257.73/min [580000], rate=35080.65/min [590000], rate=34945.71/min [600000], rate=34849.95/min [610000], rate=34691.94/min [620000], rate=34572.49/min [630000], rate=34426.23/min [640000], rate=34316.35/min [650000], rate=34210.53/min [660000], rate=34079.17/min [670000], rate=34038.95/min [680000], rate=34000.00/min [690000], rate=33962.26/min [700000], rate=33762.06/min [710000], rate=33596.21/min [720000], rate=33488.37/min [730000], rate=33409.61/min [740000], rate=33358.38/min [750000], rate=33284.02/min [760000], rate=33284.67/min [770000], rate=33309.30/min [780000], rate=33357.09/min [790000], rate=33427.36/min [800000], rate=33660.59/min [810000], rate=33962.26/min [820000], rate=34024.90/min [830000], rate=34039.64/min [840000], rate=34077.08/min [850000], rate=34090.91/min [860000], rate=34104.43/min [870000], rate=34117.65/min [880000], rate=34152.65/min [890000], rate=34186.94/min [900000], rate=34220.53/min [910000], rate=34274.95/min [920000], rate=34307.02/min [930000], rate=34359.61/min [940000], rate=34390.24/min [950000], rate=34420.29/min [960000], rate=34449.76/min [970000], rate=34601.66/min [980000], rate=34792.90/min [990000], rate=34982.33/min [1000000], rate=35190.62/min [1010000], rate=35397.20/min [1020000], rate=35622.82/min [1030000], rate=35826.09/min [1040000], rate=36006.92/min [1050000], rate=36186.10/min [1060000], rate=36363.64/min [1070000], rate=36498.01/min [1080000], rate=36610.17/min [1090000], rate=36741.57/min [1100000], rate=36892.12/min [1110000], rate=37041.16/min [1120000], rate=37188.71/min [1130000], rate=37355.37/min [1140000], rate=37500.00/min [1150000], rate=37684.33/min [1160000], rate=37846.66/min [1170000], rate=37864.08/min [1180000], rate=37840.73/min [1190000], rate=37857.90/min [1200000], rate=37894.74/min [1210000], rate=37931.03/min [1220000], rate=37966.80/min [1230000], rate=37982.50/min [1240000], rate=38134.29/min [1250000], rate=38265.31/min [1260000], rate=38356.16/min [1270000], rate=38484.85/min [1280000], rate=38592.96/min [1290000], rate=38700.00/min [1300000], rate=38922.16/min [1310000], rate=39123.94/min [1320000], rate=39285.71/min [1330000], rate=39407.41/min [1340000], rate=39547.47/min [1350000], rate=39647.58/min [1360000], rate=39785.47/min [1370000], rate=39980.54/min [1380000], rate=40174.67/min [1390000], rate=40328.82/min [1400000], rate=40520.98/min [1410000], rate=40692.64/min [1420000], rate=40882.92/min [1430000], rate=41072.28/min [1440000], rate=41260.74/min [1450000], rate=41428.57/min [1460000], rate=41575.70/min [1470000], rate=41702.13/min [1480000], rate=41847.31/min [1490000], rate=41991.55/min [1500000], rate=42154.57/min [1510000], rate=42296.92/min [1520000], rate=42438.34/min [1530000], rate=42618.38/min [1540000], rate=42797.59/min [1550000], rate=42936.29/min [1560000], rate=43074.09/min [1570000], rate=43191.20/min [1580000], rate=43267.91/min [1590000], rate=43363.64/min [1600000], rate=43458.58/min [1610000], rate=43552.75/min [1620000], rate=43685.39/min [1630000], rate=43797.58/min [1640000], rate=43617.02/min [1650000], rate=43497.36/min [1660000], rate=43379.79/min [1670000], rate=43301.64/min [1680000], rate=43206.17/min [1690000], rate=43130.58/min [1700000], rate=43074.32/min [1710000], rate=43073.05/min [1720000], rate=43035.86/min [1730000], rate=43016.99/min [1740000], rate=42980.65/min [1750000], rate=42219.54/min [1760000], rate=41954.71/min [1770000], rate=41778.13/min [1780000], rate=41637.43/min [1790000], rate=41515.27/min [1800000], rate=41411.04/min [1810000], rate=41339.93/min [1820000], rate=41363.64/min [1830000], rate=41449.60/min [1840000], rate=41379.31/min [1850000], rate=41325.39/min [1860000], rate=41287.46/min [1870000], rate=41174.31/min [1880000], rate=41107.87/min [1890000], rate=41057.20/min [1900000], rate=41021.95/min [1910000], rate=40987.12/min [1920000], rate=40967.28/min [1930000], rate=40991.15/min [1940000], rate=41000.35/min [1950000], rate=41038.23/min [1960000], rate=41047.12/min [1970000], rate=41084.46/min [1980000], rate=41121.50/min [1990000], rate=41172.41/min [2000000], rate=41194.64/min [2010000], rate=41230.77/min [2020000], rate=41280.65/min [2030000], rate=41344.20/min [2040000], rate=41407.31/min [2050000], rate=41442.05/min [2060000], rate=41490.43/min [2070000], rate=41566.27/min [2080000], rate=41669.45/min [2090000], rate=41772.15/min [2100000], rate=41860.47/min [2110000], rate=41962.21/min [2120000], rate=42091.33/min [2130000], rate=42192.14/min [2140000], rate=42306.43/min [2150000], rate=42378.45/min [2160000], rate=42352.94/min [2170000], rate=42300.19/min [2180000], rate=42302.72/min [2190000], rate=42305.22/min [2200000], rate=42307.69/min [2210000], rate=42323.65/min [2220000], rate=42339.48/min -building interval tree based on /tmp/nxf.S9Grg66SOP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=80000.00/min [30000], rate=81818.18/min [40000], rate=82758.62/min [50000], rate=83333.33/min [60000], rate=72000.00/min [70000], rate=66666.67/min [80000], rate=63157.89/min [90000], rate=61363.64/min [100000], rate=60606.06/min [110000], rate=60550.46/min [120000], rate=60000.00/min [130000], rate=60000.00/min [140000], rate=59574.47/min [150000], rate=58823.53/min [160000], rate=58536.59/min [170000], rate=58959.54/min [180000], rate=59340.66/min [190000], rate=60000.00/min [200000], rate=60606.06/min [210000], rate=61165.05/min [220000], rate=61971.83/min [230000], rate=62443.44/min [240000], rate=63157.89/min [250000], rate=63559.32/min [260000], rate=64197.53/min [270000], rate=65060.24/min [280000], rate=66666.67/min [290000], rate=67968.75/min [300000], rate=68702.29/min [310000], rate=65492.96/min [320000], rate=62745.10/min [330000], rate=61682.24/min [340000], rate=60534.12/min [350000], rate=57065.22/min [360000], rate=53865.34/min [370000], rate=53237.41/min [380000], rate=53023.26/min [390000], rate=52348.99/min [400000], rate=51502.15/min [410000], rate=51143.45/min [420000], rate=50602.41/min [430000], rate=50489.24/min [440000], rate=50769.23/min [450000], rate=51039.70/min [460000], rate=50549.45/min [470000], rate=50810.81/min [480000], rate=51154.53/min [490000], rate=51398.60/min [500000], rate=51635.11/min [510000], rate=52218.43/min [520000], rate=52702.70/min [530000], rate=53088.48/min [540000], rate=53289.47/min [550000], rate=53398.06/min [560000], rate=52996.85/min [570000], rate=52534.56/min [580000], rate=51403.25/min [590000], rate=50000.00/min [600000], rate=48714.48/min [610000], rate=47286.82/min [620000], rate=46153.85/min [630000], rate=45487.36/min [640000], rate=44703.14/min [650000], rate=44469.78/min [660000], rate=44494.38/min [670000], rate=44469.03/min [680000], rate=44590.16/min [690000], rate=44660.19/min [700000], rate=44680.85/min [710000], rate=44747.90/min [720000], rate=44582.04/min [730000], rate=44064.39/min [740000], rate=43444.23/min [750000], rate=42775.67/min [760000], rate=42418.60/min [770000], rate=41847.83/min [780000], rate=41197.18/min [790000], rate=40791.74/min [800000], rate=40268.46/min [810000], rate=39967.11/min [820000], rate=39935.06/min [830000], rate=39492.47/min [840000], rate=39467.50/min [850000], rate=39688.72/min [860000], rate=39876.35/min [870000], rate=40030.67/min [880000], rate=40060.70/min [890000], rate=40060.02/min [900000], rate=39940.83/min [910000], rate=40029.33/min [920000], rate=40145.45/min [930000], rate=40143.88/min [940000], rate=40343.35/min [950000], rate=40540.54/min [960000], rate=40793.20/min [970000], rate=41014.80/min [980000], rate=41263.16/min [990000], rate=41509.43/min [1000000], rate=41695.62/min [1010000], rate=41478.44/min [1020000], rate=41239.89/min [1030000], rate=40738.30/min [1040000], rate=39669.42/min [1050000], rate=38793.10/min [1060000], rate=37970.15/min [1070000], rate=37456.24/min [1080000], rate=37262.79/min [1090000], rate=37180.22/min [1100000], rate=36605.66/min [1110000], rate=36195.65/min [1120000], rate=36206.90/min [1130000], rate=36256.68/min [1140000], rate=36305.73/min [1150000], rate=36315.79/min [1160000], rate=36363.64/min [1170000], rate=36391.91/min [1180000], rate=36438.50/min [1190000], rate=36484.41/min [1200000], rate=36529.68/min [1210000], rate=36574.31/min [1220000], rate=36600.00/min [1230000], rate=36679.92/min [1240000], rate=36813.46/min [1250000], rate=36909.45/min [1260000], rate=37004.41/min [1270000], rate=37098.34/min [1280000], rate=37209.30/min [1290000], rate=37319.19/min [1300000], rate=37428.02/min [1310000], rate=37535.82/min [1320000], rate=37624.70/min [1330000], rate=37694.85/min [1340000], rate=37781.95/min [1350000], rate=37885.87/min [1360000], rate=37953.49/min [1370000], rate=38037.95/min [1380000], rate=38139.11/min [1390000], rate=38221.81/min [1400000], rate=38009.05/min [1410000], rate=37801.61/min [1420000], rate=37715.80/min [1430000], rate=37730.87/min [1440000], rate=37516.28/min [1450000], rate=37307.03/min [1460000], rate=36915.30/min [1470000], rate=36658.35/min [1480000], rate=36483.16/min [1490000], rate=36356.24/min [1500000], rate=36407.77/min [1510000], rate=36444.09/min [1520000], rate=36553.11/min [1530000], rate=36646.71/min [1540000], rate=36710.37/min [1550000], rate=36744.37/min [1560000], rate=36806.92/min [1570000], rate=36883.32/min [1580000], rate=36915.89/min [1590000], rate=36976.74/min [1600000], rate=37065.64/min [1610000], rate=37111.03/min [1620000], rate=37184.39/min [1630000], rate=37228.78/min [1640000], rate=37300.99/min [1650000], rate=37386.71/min [1660000], rate=37429.54/min [1670000], rate=37485.97/min [1680000], rate=37583.89/min [1690000], rate=37667.16/min [1700000], rate=37707.95/min [1710000], rate=37790.06/min [1720000], rate=37843.78/min [1730000], rate=37897.04/min [1740000], rate=37894.74/min [1750000], rate=37878.79/min [1760000], rate=37903.80/min [1770000], rate=37928.57/min [1780000], rate=37953.09/min [1790000], rate=38017.70/min [1800000], rate=38054.97/min [1810000], rate=38118.64/min [1820000], rate=38155.14/min [1830000], rate=38178.03/min [1840000], rate=38227.15/min [1850000], rate=38289.07/min [1860000], rate=38337.34/min [1870000], rate=38398.36/min [1880000], rate=38485.16/min [1890000], rate=38571.43/min [1900000], rate=38670.28/min [1910000], rate=38781.73/min [1920000], rate=38879.51/min [1930000], rate=38963.66/min [1940000], rate=39060.40/min [1950000], rate=39156.63/min [1960000], rate=39265.44/min [1970000], rate=39360.64/min [1980000], rate=39468.44/min [1990000], rate=39536.42/min [2000000], rate=39630.12/min [2010000], rate=39736.41/min [2020000], rate=39829.12/min [2030000], rate=39908.26/min [2040000], rate=40013.08/min [2050000], rate=40104.34/min [2060000], rate=40208.20/min [2070000], rate=40311.59/min [2080000], rate=40414.51/min [2090000], rate=40477.73/min [2100000], rate=40294.21/min [2110000], rate=40139.51/min [2120000], rate=40012.58/min [2130000], rate=39925.02/min [2140000], rate=39851.02/min [2150000], rate=39765.72/min [2160000], rate=39730.23/min [2170000], rate=39719.34/min [2180000], rate=39684.47/min [2190000], rate=39685.90/min [2200000], rate=39699.25/min [2210000], rate=39700.60/min -building interval tree based on /tmp/nxf.S9Grg66SOP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=40000.00/min [20000], rate=46153.85/min [30000], rate=50000.00/min [40000], rate=51063.83/min [50000], rate=53571.43/min [60000], rate=54545.45/min [70000], rate=56000.00/min [80000], rate=57142.86/min [90000], rate=58695.65/min [100000], rate=60606.06/min [110000], rate=61682.24/min [120000], rate=61538.46/min [130000], rate=60000.00/min [140000], rate=58741.26/min [150000], rate=59210.53/min [160000], rate=60759.49/min [170000], rate=60714.29/min [180000], rate=59016.39/min [190000], rate=57286.43/min [200000], rate=56338.03/min [210000], rate=55506.61/min [220000], rate=54098.36/min [230000], rate=50922.51/min [240000], rate=49484.54/min [250000], rate=48701.30/min [260000], rate=48447.20/min [270000], rate=48071.22/min [280000], rate=47863.25/min [290000], rate=45194.81/min [300000], rate=44665.01/min [310000], rate=44497.61/min [320000], rate=43636.36/min [330000], rate=43231.44/min [340000], rate=41803.28/min [350000], rate=40618.96/min [360000], rate=39705.88/min [370000], rate=38743.46/min [380000], rate=38190.95/min [390000], rate=37925.45/min [400000], rate=37617.55/min [410000], rate=37788.02/min [420000], rate=38297.87/min [430000], rate=38680.66/min [440000], rate=39053.25/min [450000], rate=39301.31/min [460000], rate=39655.17/min [470000], rate=40056.82/min [480000], rate=40449.44/min [490000], rate=40833.33/min [500000], rate=41208.79/min [510000], rate=41689.37/min [520000], rate=42105.26/min [530000], rate=42456.61/min [540000], rate=42744.06/min [550000], rate=42746.11/min [560000], rate=42802.55/min [570000], rate=42170.16/min [580000], rate=40989.40/min [590000], rate=39597.32/min [600000], rate=38543.90/min [610000], rate=37693.10/min [620000], rate=36868.19/min [630000], rate=36521.74/min [640000], rate=35988.75/min [650000], rate=35358.11/min [660000], rate=34524.85/min [670000], rate=33781.51/min [680000], rate=33009.71/min [690000], rate=32343.75/min [700000], rate=31722.05/min [710000], rate=31254.59/min [720000], rate=30857.14/min [730000], rate=30458.97/min [740000], rate=30060.93/min [750000], rate=29761.90/min [760000], rate=29495.47/min [770000], 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