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/a9/f4fbb6b0660b3578bfc3e21347cf83/aih-tih-sc-9114fc-R1_B23WHYVLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/bd85aa93cb0d2979d1df5827fa6010/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/bd85aa93cb0d2979d1df5827fa6010/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/f4fbb6b0660b3578bfc3e21347cf83/aih-tih-sc-9114fc-R1_B23WHYVLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/9933eb86bcf10fa0f19f320406e7bc/aih-tih-sc-9114fc-R1_B23WHYVLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.sLmm2wFczb/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.sLmm2wFczb/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.sLmm2wFczb/./star-fusion.preliminary -sample contains 295079004 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.sLmm2wFczb/ctat_genome_lib_build_dir -J /tmp/nxf.sLmm2wFczb/aih-tih-sc-9114fc-R1_B23WHYVLT4_1.Chimeric.out.junction -O /tmp/nxf.sLmm2wFczb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.sLmm2wFczb/aih-tih-sc-9114fc-R1_B23WHYVLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.sLmm2wFczb/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=54545.45/min [20000], rate=60000.00/min [30000], rate=62068.97/min [40000], rate=60000.00/min [50000], rate=61224.49/min [60000], rate=64285.71/min [70000], rate=65625.00/min [80000], rate=67605.63/min [90000], rate=69230.77/min [100000], rate=66666.67/min [110000], rate=60000.00/min [120000], rate=56692.91/min [130000], rate=52702.70/min [140000], rate=50299.40/min [150000], rate=49450.55/min [160000], rate=48979.59/min [170000], rate=48341.23/min [180000], rate=47787.61/min [190000], rate=47899.16/min [200000], rate=47808.76/min [210000], rate=47727.27/min [220000], rate=47826.09/min [230000], rate=47916.67/min [240000], rate=48000.00/min [250000], rate=48543.69/min [260000], rate=48598.13/min [270000], rate=48648.65/min [280000], rate=48979.59/min [290000], rate=49291.78/min [300000], rate=49723.76/min [310000], rate=50134.77/min [320000], rate=50526.32/min [330000], rate=50769.23/min [340000], rate=51256.28/min [350000], rate=51597.05/min [360000], rate=52048.19/min [370000], rate=52482.27/min [380000], rate=52777.78/min [390000], rate=53061.22/min [400000], rate=53452.12/min [410000], rate=53829.32/min [420000], rate=54193.55/min [430000], rate=54661.02/min [440000], rate=55114.82/min [450000], rate=55555.56/min [460000], rate=55983.77/min [470000], rate=56400.00/min [480000], rate=56804.73/min [490000], rate=57087.38/min [500000], rate=57471.26/min [510000], rate=56983.24/min [520000], rate=56624.32/min [530000], rate=55985.92/min [540000], rate=55574.61/min [550000], rate=55369.13/min [560000], rate=55172.41/min [570000], rate=55072.46/min [580000], rate=55063.29/min [590000], rate=55054.43/min [600000], rate=54961.83/min [610000], rate=54872.56/min [620000], rate=54705.88/min [630000], rate=54782.61/min [640000], rate=54468.09/min [650000], rate=54166.67/min [660000], rate=53877.55/min [670000], rate=53386.45/min [680000], rate=53055.92/min [690000], rate=52873.56/min [700000], rate=52565.71/min [710000], rate=52269.94/min [720000], rate=52173.91/min [730000], rate=52080.86/min [740000], rate=51869.16/min [750000], rate=51783.66/min [760000], rate=51759.36/min [770000], rate=51677.85/min [780000], rate=51712.71/min [790000], rate=51803.28/min [800000], rate=51835.85/min [810000], rate=51923.08/min [820000], rate=52008.46/min [830000], rate=52146.60/min [840000], rate=52336.45/min [850000], rate=52469.14/min [860000], rate=52653.06/min [870000], rate=52834.01/min [880000], rate=53012.05/min [890000], rate=53187.25/min [900000], rate=53412.46/min [910000], rate=53581.94/min [920000], rate=53801.17/min [930000], rate=53602.31/min [940000], rate=52908.07/min [950000], rate=52245.65/min [960000], rate=51612.90/min [970000], rate=51097.45/min [980000], rate=50558.90/min [990000], rate=50126.58/min [1000000], rate=49668.87/min [1010000], rate=49308.38/min [1020000], rate=48999.20/min [1030000], rate=48699.76/min [1040000], rate=48484.85/min [1050000], rate=48275.86/min [1060000], rate=48218.35/min [1070000], rate=48125.94/min [1080000], rate=48000.00/min [1090000], rate=47912.09/min [1100000], rate=47791.46/min [1110000], rate=47741.94/min [1120000], rate=47659.57/min [1130000], rate=47645.82/min [1140000], rate=47665.51/min [1150000], rate=47586.21/min [1160000], rate=47606.02/min [1170000], rate=47657.84/min [1180000], rate=47741.07/min [1190000], rate=47727.27/min [1200000], rate=47713.72/min [1210000], rate=47669.07/min [1220000], rate=47656.25/min [1230000], rate=47705.24/min [1240000], rate=47753.53/min [1250000], rate=47862.16/min [1260000], rate=48030.50/min [1270000], rate=48136.45/min [1280000], rate=48241.21/min [1290000], rate=48314.61/min [1300000], rate=48387.10/min [1310000], rate=48458.69/min [1320000], rate=48529.41/min [1330000], rate=48658.54/min [1340000], rate=48756.82/min [1350000], rate=48883.52/min [1360000], rate=49038.46/min [1370000], rate=49162.68/min [1380000], rate=49285.71/min [1390000], rate=49466.19/min [1400000], rate=49704.14/min [1410000], rate=49852.68/min [1420000], rate=49970.67/min [1430000], rate=50087.57/min [1440000], rate=50232.56/min [1450000], rate=50318.10/min [1460000], rate=50200.57/min [1470000], rate=50113.64/min [1480000], rate=50000.00/min [1490000], rate=49944.13/min [1500000], rate=49889.14/min [1510000], rate=49862.41/min [1520000], rate=49836.07/min [1530000], rate=49810.09/min [1540000], rate=49811.32/min [1550000], rate=49785.87/min [1560000], rate=49813.73/min [1570000], rate=49841.27/min [1580000], rate=49868.49/min [1590000], rate=49895.40/min [1600000], rate=49947.97/min [1610000], rate=50025.89/min [1620000], rate=50077.28/min [1630000], rate=50153.85/min [1640000], rate=50204.08/min [1650000], rate=50253.81/min [1660000], rate=50353.89/min [1670000], rate=50427.78/min [1680000], rate=50551.65/min [1690000], rate=50624.06/min [1700000], rate=50746.27/min [1710000], rate=50867.63/min [1720000], rate=50962.96/min [1730000], rate=51107.83/min [1740000], rate=51251.84/min [1750000], rate=51420.18/min [1760000], rate=51612.90/min [1770000], rate=51754.39/min [1780000], rate=51945.53/min [1790000], rate=52085.35/min [1800000], rate=52249.64/min [1810000], rate=52413.13/min [1820000], rate=52575.83/min [1830000], rate=52737.75/min [1840000], rate=52898.90/min [1850000], rate=53033.92/min [1860000], rate=53218.88/min [1870000], rate=53352.35/min [1880000], rate=53485.06/min [1890000], rate=53617.02/min [1900000], rate=53722.90/min [1910000], rate=53828.09/min [1920000], rate=53932.58/min [1930000], rate=54011.19/min [1940000], rate=54114.37/min [1950000], rate=54191.76/min [1960000], rate=54044.12/min [1970000], rate=53947.97/min [1980000], rate=53804.35/min [1990000], rate=53687.05/min [2000000], rate=53619.30/min [2010000], rate=53528.63/min [2020000], rate=53462.73/min [2030000], rate=53397.63/min [2040000], rate=53379.85/min [2050000], rate=53339.12/min [2060000], rate=53275.86/min [2070000], rate=53259.01/min [2080000], rate=53287.79/min [2090000], rate=53316.33/min [2100000], rate=53322.05/min [2110000], rate=53350.19/min [2120000], rate=53378.09/min [2130000], rate=53428.09/min [2140000], rate=53477.72/min [2150000], rate=53504.77/min [2160000], rate=53553.72/min [2170000], rate=53624.38/min [2180000], rate=53716.63/min [2190000], rate=53786.33/min [2200000], rate=53877.55/min [2210000], rate=53946.30/min [2220000], rate=54014.60/min [2230000], rate=54104.33/min [2240000], rate=54193.55/min [2250000], rate=54260.45/min [2260000], rate=54348.70/min [2270000], rate=54327.88/min [2280000], rate=54242.66/min [2290000], rate=54158.45/min [2300000], rate=54075.24/min [2310000], rate=54035.09/min [2320000], rate=54016.30/min [2330000], rate=53956.00/min [2340000], rate=53917.05/min [2350000], rate=53899.08/min [2360000], rate=53901.79/min [2370000], rate=53924.91/min [2380000], rate=53927.49/min [2390000], rate=53930.05/min [2400000], rate=53932.58/min [2410000], rate=53975.36/min [2420000], rate=53957.64/min [2430000], rate=54000.00/min [2440000], rate=54042.08/min [2450000], rate=54083.89/min [2460000], rate=54165.14/min [2470000], rate=54206.29/min [2480000], rate=54286.76/min [2490000], rate=54366.81/min [2500000], rate=54446.46/min [2510000], rate=54505.97/min [2520000], rate=54545.45/min -building interval tree based on /tmp/nxf.sLmm2wFczb/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=75000.00/min [30000], rate=60000.00/min [40000], rate=63157.89/min [50000], rate=65217.39/min [60000], rate=66666.67/min [70000], rate=68852.46/min [80000], rate=68571.43/min [90000], rate=71052.63/min [100000], rate=72289.16/min [110000], rate=74157.30/min [120000], rate=75789.47/min [130000], rate=76470.59/min [140000], rate=78504.67/min [150000], rate=79646.02/min [160000], rate=75000.00/min [170000], rate=66666.67/min [180000], rate=62790.70/min [190000], rate=60000.00/min [200000], rate=57971.01/min [210000], rate=56000.00/min [220000], rate=54545.45/min [230000], rate=53076.92/min [240000], rate=51985.56/min [250000], rate=51369.86/min [260000], rate=50649.35/min [270000], rate=50000.00/min [280000], rate=49411.76/min [290000], rate=48739.50/min [300000], rate=48257.37/min [310000], rate=47814.91/min [320000], rate=47290.64/min [330000], rate=46808.51/min [340000], rate=46575.34/min [350000], rate=46153.85/min [360000], rate=45957.45/min [370000], rate=45773.20/min [380000], rate=45600.00/min [390000], rate=45261.12/min [400000], rate=45112.78/min [410000], rate=45054.95/min [420000], rate=45000.00/min [430000], rate=44482.76/min [440000], rate=44295.30/min [450000], rate=44045.68/min [460000], rate=43949.04/min [470000], rate=43925.23/min [480000], rate=44036.70/min [490000], rate=44011.98/min [500000], rate=44052.86/min [510000], rate=44092.22/min [520000], rate=44130.13/min [530000], rate=44166.67/min [540000], rate=44081.63/min [550000], rate=44000.00/min [560000], rate=43979.06/min [570000], rate=44015.44/min [580000], rate=43994.94/min [590000], rate=43975.16/min [600000], rate=44063.65/min [610000], rate=44096.39/min [620000], rate=44075.83/min [630000], rate=44210.53/min [640000], rate=44341.80/min [650000], rate=44419.13/min [660000], rate=44594.59/min [670000], rate=44866.07/min [680000], rate=45082.87/min [690000], rate=45245.90/min [700000], rate=45405.41/min [710000], rate=45659.16/min [720000], rate=45908.61/min [730000], rate=46153.85/min [740000], rate=46346.56/min [750000], rate=46583.85/min [760000], rate=46817.25/min [770000], rate=46998.98/min [780000], rate=47320.53/min [790000], rate=47590.36/min [800000], rate=47808.76/min [810000], rate=48023.72/min [820000], rate=48282.63/min [830000], rate=48443.58/min [840000], rate=48368.52/min [850000], rate=48341.23/min [860000], rate=48359.89/min [870000], rate=48333.33/min [880000], rate=48351.65/min [890000], rate=48369.57/min [900000], rate=48430.49/min [910000], rate=48447.20/min [920000], rate=48506.15/min [930000], rate=48563.97/min [940000], rate=48704.66/min [950000], rate=48801.37/min [960000], rate=48896.43/min [970000], rate=49031.17/min [980000], rate=49122.81/min [990000], rate=49253.73/min [1000000], rate=49382.72/min [1010000], rate=49550.29/min [1020000], rate=49715.68/min [1030000], rate=49838.71/min [1040000], rate=50000.00/min [1050000], rate=50119.33/min [1060000], rate=50276.68/min [1070000], rate=50392.46/min [1080000], rate=50546.02/min [1090000], rate=50737.01/min [1100000], rate=50925.93/min [1110000], rate=51112.82/min [1120000], rate=51297.71/min [1130000], rate=51441.58/min [1140000], rate=51467.27/min [1150000], rate=51646.71/min [1160000], rate=51940.30/min [1170000], rate=52154.53/min [1180000], rate=52522.26/min [1190000], rate=52654.87/min [1200000], rate=52902.28/min [1210000], rate=53109.00/min [1220000], rate=53275.11/min [1230000], rate=53323.70/min [1240000], rate=53448.28/min [1250000], rate=53533.19/min [1260000], rate=53807.83/min [1270000], rate=53966.01/min [1280000], rate=54275.62/min [1290000], rate=54430.38/min [1300000], rate=54545.45/min [1310000], rate=54811.72/min [1320000], rate=55076.50/min [1330000], rate=55378.21/min [1340000], rate=55524.86/min [1350000], rate=55746.73/min [1360000], rate=55928.72/min [1370000], rate=56147.54/min [1380000], rate=56364.87/min [1390000], rate=56542.37/min [1400000], rate=56527.59/min [1410000], rate=56664.43/min [1420000], rate=56724.37/min [1430000], rate=56972.11/min [1440000], rate=57105.09/min [1450000], rate=57350.03/min [1460000], rate=57555.85/min [1470000], rate=57722.51/min [1480000], rate=57887.87/min [1490000], rate=58089.67/min [1500000], rate=58177.12/min [1510000], rate=58226.22/min [1520000], rate=58274.76/min [1530000], rate=58359.82/min [1540000], rate=58481.01/min [1550000], rate=58564.23/min [1560000], rate=58646.62/min [1570000], rate=58764.82/min [1580000], rate=58845.44/min [1590000], rate=59071.21/min [1600000], rate=59222.70/min [1610000], rate=59373.08/min [1620000], rate=59304.45/min [1630000], rate=59416.77/min [1640000], rate=59348.61/min [1650000], rate=59352.52/min [1660000], rate=59391.77/min [1670000], rate=59395.38/min [1680000], rate=59363.96/min [1690000], rate=59402.46/min [1700000], rate=59440.56/min [1710000], rate=59512.76/min [1720000], rate=59618.72/min [1730000], rate=59689.48/min [1740000], rate=59725.40/min [1750000], rate=59760.96/min [1760000], rate=59830.03/min [1770000], rate=59730.03/min [1780000], rate=59798.43/min [1790000], rate=59832.87/min [1800000], rate=59900.17/min [1810000], rate=59966.87/min [1820000], rate=60032.99/min [1830000], rate=60131.43/min [1840000], rate=60196.29/min [1850000], rate=60260.59/min [1860000], rate=60324.32/min [1870000], rate=60420.03/min [1880000], rate=60482.57/min [1890000], rate=60351.25/min [1900000], rate=59623.43/min [1910000], rate=58890.03/min [1920000], rate=58093.80/min [1930000], rate=57383.55/min [1940000], rate=56891.50/min [1950000], rate=56277.06/min [1960000], rate=55866.98/min [1970000], rate=55285.31/min [1980000], rate=55102.04/min [1990000], rate=55073.80/min [2000000], rate=54669.70/min [2010000], rate=54275.43/min [2020000], rate=53914.59/min [2030000], rate=53491.44/min [2040000], rate=53101.95/min [2050000], rate=52609.07/min [2060000], rate=52306.39/min [2070000], rate=51966.53/min [2080000], rate=51677.02/min [2090000], rate=51456.71/min [2100000], rate=51365.67/min [2110000], rate=51130.86/min [2120000], rate=50920.74/min [2130000], rate=50754.57/min [2140000], rate=50650.89/min [2150000], rate=50509.01/min [2160000], rate=50447.64/min [2170000], rate=50348.03/min [2180000], rate=50249.71/min [2190000], rate=50190.99/min [2200000], rate=50151.98/min [2210000], rate=50151.29/min [2220000], rate=50131.73/min [2230000], rate=50112.36/min [2240000], rate=50111.86/min [2250000], rate=50092.76/min [2260000], rate=50129.39/min [2270000], rate=50147.28/min [2280000], rate=50183.42/min [2290000], rate=50237.66/min [2300000], rate=50291.55/min [2310000], rate=50363.37/min [2320000], rate=50453.06/min [2330000], rate=50560.58/min [2340000], rate=50667.63/min [2350000], rate=50755.94/min [2360000], rate=50789.10/min [2370000], rate=50604.98/min [2380000], rate=50477.20/min [2390000], rate=50351.12/min [2400000], rate=50191.70/min [2410000], rate=50086.60/min [2420000], rate=49982.79/min [2430000], rate=49914.41/min [2440000], rate=49829.82/min [2450000], rate=49763.03/min [2460000], rate=49713.71/min [2470000], rate=49664.88/min [2480000], rate=49633.09/min [2490000], rate=49601.59/min [2500000], rate=49570.39/min [2510000], rate=49539.47/min [2520000], rate=49541.28/min